Opening The Door
by sarcasmqueen66
Summary: This is about a Girl OC who is asked to go to Atlantis, but not for the reason she thinks, but is there something even bigger going on that could threaten the whole of the Atlantis expedition! Now COMPLETE!
1. Chapter 1

Stepping into the dingy grey elevator, Sophie Wells tried desperately to remain calm. She glanced up to see the soldiers escorting her, loaded up with all her precious training gear. As the elevator began to descend Sophie yet again asked herself.

What does the US government want me for? Why now?

Two years ago Sophie had been an aspiring cadet, training hard to achieve a place in the Air Force. But two years ago she left, with only a few more months of training to do. Her sudden disappearance shocked all those around her. She was top in all her classes and no one could understand why she left; only she knew. Remembering this brought a shiver down her spine, she didn't want to think about that now.

The elevator doors opened after what seemed like an eternity.

We really must be deep underground she thought to herself as she stepped out of the elevator and looked around at the same grey interior as the elevator.

"I don't think I'm gonna like it here it's not Sophie mumbled.

"Don't worry you wont be staying here" a guy with grey hair in a blue air force uniform said. "I'm General Jack O'Neill. "You must be Sophie Wells nice to meet you!"

Embarrassed that he had heard she blushed slightly and said "Sorry I didn't mean it like that, and I'm grateful for the job and all. But what am I doing here?"

"There's a lot to explain, follow me there's some people I would like you to meet." He then indicated to the soldiers to take Sophie's belongings to some storage area, and led Sophie off towards the briefing room.

When they went through the door of the briefing room there were four people already sat at a large table, speaking in hushed tones, as Sophie entered, trailing the general. As soon as they noticed their arrival all conversion ended and they all looked up. There were three men and one woman, the guy with messy hair was introduced as Lt Col. John Sheppard. Next to him was a smug looking guy known as Doctor Rodney McKay. Then there was the woman Teyla Emmagen she smiled and nodded briefly. The last person to be introduced was Ronon Dex, who even though was sat down, looked over six foot tall and pure muscle, he was also who Sophie thought was hot; He however just looked up and arched his eyebrows slightly, as if unable to work Sophie out.

Sophie smiled and said a nervous hello before the general pointed to a seat opposite them. He, however, didn't take the empty seat next to her, but went and sat next to the one called Sheppard. Sophie sat there only a few seconds before curiosity got the better of her.

"So…just wondering what on earth I'm doing here?"

Col. Sheppard looked at the general and said "has she signed sir?" when the general answered with a nod, Sheppard looked back at Sophie and said,

"There's a lot we need to tell you and we need you to hear all of it, is that ok?"

When Sophie gave her approval he launched into revealing the secret of Atlantis to her. Not to mention the stargate as well.

Later on Sophie sat in the room she had been assigned, trying to understand all that she had heard.

"Stargates, Aliens, Wraith I mean what the hell are they?" she muttered to herself. They wanted her! Sophie did not understand this part at all. Yes she was a doctor of medicine but she had only ever practiced for a year, she had felt she wanted more of a physical challenge. So Sophie had then turned her attention to martial arts and fitness. She learned and mastered as many types as she could, then trained to be a long distance runner and ran marathons. Again Sophie grew bored, and began her training as a cadet, where she left with months left, nobody however knew why. Sophie is only 27 years old still relatively young to have achieved so much. However learning was one of Sophie's most important skills she had always fast tracked her way through almost every course she ever took, all but one.

Sophie knew she had a big decision ahead of her. She had sat through the briefing trying to take everything in, but it was hard, the concept of travelling to another galaxy that was hardest. But there was something in that sentence that made more sense than anything had ever done. That was how she knew that she must go and face a challenge like no other.

The next morning as she was eating her breakfast in the mess hall, General O'Neill sat opposite her and said

"So I guess you want to know what we want you to do at Atlantis, don't you?"

When Sophie nodded that she did the general continued,

"Well you have a few qualifications in different fields so we would like you to use them all, but your official role will be a Fitness Trainer of sorts. You see we need all of the people on Atlantis to be able to fight in hand to hand combat, and be physically, well…fit. So it will be your responsibility to deal with this issue. You will be working along side our team of medical doctors as well…so what do you say? You in?"

Sophie looked straight at the general and said "yes…yes I am!"

"Good, welcome! You leave in an hour."

An hour later Sophie stood opened mouthed, staring at the event horizon of the stargate. Teyla walked up to her and smiled reassuringly don't be afraid all you have to do is walk through it"

Sophie took a deep breath and stepped into it, enveloped in the shimmering surface of the event horizon.

When she arrived on the other side, Sophie was mesmerised by what she saw the inside of the place she had stepped into was like nothing she had ever seen before.

For once she was lost for words "I…uh…wow"

"Pretty nice huh?" Sheppard said from where he was standing, about three metres away, and facing her. Next to him was a blonde woman who introduced herself as Col. Samantha Carter, the leader of Atlantis. A few words of greeting were exchanged and Col. Carter then asked Ronon -who had remained silent since Sophie had met him- to help her carry her stuff to her quarters as it was across the hall from his.

The walk there was silent. Not that Sophie minded, Atlantis was amazing and the views from some of its windows well defied words. When they arrived Sophie was amazed at the view form her quarters,although she had to admit it was pretty good inside, as she sneaked a glance at her guide as he put down the bags he was carrying. There where actually only two and Sophie knew she could have managed them alone.

"Is this all your stuff? You don't seem to have much. "

His voice it makes her jump it's the first time she's heard it. He doesn't seem to however notice her shock, so she just says.

"Well I…err…don't have a lot of stuff you see that's mainly training stuff."

Ronon nodded and said "I shall show you to the mess hall and you can have lunch if you want?"

Sophie nodded and told him that would be great.


	2. Chapter 2

Chapter 2

It had been almost a week now since Sophie Wells had arrived on Atlantis, she had spent a lot of time in her quarters reading personal files, and preparing the timetable for her training sessions with the residents of Atlantis.

The only time Sophie had actually left her quarters was to eat, or meet with Colonel Carter to discuss her ideas.

That morning Sophie had took a complete plan of what she intended to do, to Col. Carter. She intended to teach self-defence to all the residents in Atlantis, and doing so in groups. To ensure the residents were able to make these classes she arranged a number of different times for them to sign up to the most appropriate class for them.

These classes were, however, mandatory and Sophie knew some people were not going to like it.

Col. Carter immediately liked the idea and implemented it straight away.

A week later Sophie arrived in the gym for her first session only to find Colonel Sheppard, Teyla and Ronon already there.

As she entered Teyla smiled and said,

"Sophie, we are thoroughly looking forward to your first session!"

"But…you three don't have to come, Colonel Carter has already assured me that you are all exceptionally well trained in both defence and attack when it comes hand to hand combat!"

Sheppard looked amused and gave a cheeky grin and replied

"But that gives us a head start to being the teachers pet!"

At this both Ronon and Teyla looked confused and it took Sophie a moment to remember that they were not from Earth, but a different galaxy completely.

Sheppard began to explain when the door to the gym opened, a stone faced Rodney entered with a trail of nervous scientists.

Immediately he began complaining but a glare from Sheppard and a warning to show respect from Teyla silenced him.

Sophie had originally planned on having a gentle first session, but Rodney had annoyed her with his attitude when just walking through the door. So her opening speech was altered to a much harsher version. Sophie faced the group of twenty people and began.

"My name is Sophie and I will be teaching you self defence. These sessions are mandatory as I know you have been made fully aware. If you skip one of my classes without good reason; a good reason that is given to me directly from your superior officer, you will live to regret it!"

When saying this last part she added a particular stony glare at her suspects that would be first to cut class, Rodney included.

"Now lets begin, first off we shall do some endurance training. Which will give me an idea of how fit you all are. Ok, follow me!"

Sophie left the gym at a slow placed jog.

Throughout the jog which lasted about fifteen minutes, Sophie noticed that Teyla, Sheppard and Ronon all kept easily up with her. So when they arrived back at the gym, she was not surprised to find that no-one else followed the four of them in.

Shaking her head she opened her mouth to speak, when a slightly out of breath Sheppard got there first.

"You call that endurance training? You should join me and Ronon. I for one can hardly keep up with him!"

Sophie however was caught by surprise when the next person who spoke was in fact Ronon.

"Tonight seven o'clock. If you think you can keep up!"

Ever since arriving on Atlantis two weeks ago, Sophie had eaten her meals with the team. That is when they were not off world.

Still she had noticed that Ronon spoke very little and only spoke when it was important.

However this was the second time he had spoken out of character to her. Maybe he was staring to like her, or even trust her.

Sophie remembered back to the conversation she had with Teyla one evening.

Teyla had explained of her past and her people. When Sophie had asked about Ronon, Teyla said she would prefer it if Sophie asked him herself. She did however inform her that he found it difficult to trust and to not be put off by his awkwardness at first.

This had left Sophie wondering what had he been through.

Dragging herself away from the thought she answered.

"Sure, I'm sure I shall keep up."

Before anymore could be said the gym doors opened and the rest of the group dragged themselves in looking miserable and out of breath.

"Ok, well it looks like you all need to work on that! So at the beginning or end of every lesson we shall go for a run."

Ignoring the disgruntled looks from the scientists especially McKay. She continued.

"Right then I would like you to get into pairs."

She watched as the scientists scurried around pairing up. Ronon paired with Teyla and Sheppard grabbed McKay and immediately began speaking in a hushed voice to him. By McKay's face and the solemn "Do I have to?" This told Sophie clearly that he was being warned by his commanding officer.

Choosing to ignore this Sophie began teaching her students a basic block.

The time passed quickly and soon it was he end of the lesson. As she was dismissing them with the instruction to practice, McKay piped up "Hey Sophie, if you're teaching us, how do we know you're a good fighter. I think you should prove it!

Murmurs of agreement surfaced from the scientists.

"McKay! I have warned you already!" John said fiercely.

Sophie however liked the idea of a challenge and questioned, "Ok then who wants to fight me?"

Sophie was just about to pick on Rodney and ask if he would, when a low gruff voice sounded.

"I will."

Sophie whirled around to see a small smile playing on the lips of Ronon Dex. There was a glint in his eyes that seemed to be daring her.

"Ok let's do this."

Sophie walked into the middle of the room and took up her simple fighting stance, Ronon joined her and the rest of the scientists and Ronon's team stood against the walls, spreading around the room.

Ronon took a swing at her, but she was prepared and she blocked it with ease.

For what seemed like an eternity they were locked in ferocious hand to hand combat. Every so often it looked as if one person was getting the upper a hand, but then it went back to a stale mate. Then Sophie managed to execute a flip that knocked Ronon to the ground, but he grabbed her waist, taking her down with him, so that she landed on top of him. Sophie smiled, thinking she was victorious.

But with unbelievable speed Ronon flipped her. Now Ronon was on top of her, with his knees either side of her hips.

This time it was his turn to smile.

"Crap! You're fast!" Sophie pointed out, which only caused Ronon to laugh a little. Ronon got up pulling her up as well.

Applause erupted throughout the room and Sophie noticed that McKay was stood there open mouthed and staring.

"Was that good enough for you McKay?" Ronon said, all the time still looking at Sophie, he then added "You're a good fighter!" to Sophie.

Sophie smiled and said thanks and told the class that they could leave. Sophie was packing up her stuff when she turned round and saw John and Teyla still standing there.

"Is there something I can do for you guys?"

Teyla glances at John and says "You are very well trained in hand to hand. I have never seen anyone come close to beating Ronon like that. I am very impressed."

Slightly embarrassed at this Sophie muttered a nervous thanks and turned to John who had began speaking.

"I was wondering if you would want to go off world sometimes. It would be to help out with sick or injured, because I know you are a doctor and you are going to help out in the infirmary, but we could do with a doctor that can protect herself. If I clear it with Col. Carter and Doctor Keller will you do it?

"Um…sure…if you want me to."

Upon hearing this John smiled and left leaving Teyla and Sophie alone.

"So me, John and Ronon train in here quite often. I would like it if you came, you know when you have the time."

Sophie agreed that she would.

Teyla gave an amused smile and walked to the door then paused to say.

"I know you're interested I can see it in your eyes…and his"

This startled Sophie, the young Athosian women certainly had an eye for things and was it true.

Was Ronon interested in her as well?

As Sophie left the gym she found herself smiling.

A new sense of hope was bubbling inside her, for the first time in months.

(A/N: Sorry it took so long! Hope you like it! Also a special thanks to Chloe!)


	3. Chapter 3

Sophie had now been on Atlantis a little over a month, splitting her time between teaching self-defense and helping in the infirmary. It hadn't been her first choice, but the infirmary needed help so she had agreed to give some.

That night, Sophie had offered to cover one of the other doctor's shifts in the infirmary, because they weren't feeling well. However this night it was empty. Sophie was sat on one of the beds reading a book. Her mind however was not on the book; instead it kept wandering to back to the events of the last month.

A brief smile crossed her face as she reflected on the first self-defense lesson, that fight with Ronon had been exhilarating.

Ronon had invited her to run with him and Sheppard, which she had the very next day. She was just going into her room when Ronon came out of his and asked if she felt like joining them.

Sophie joined them, wondering if she would be able to keep up. She had said she could, but she had begun wondering if she would. The run had been fun and she had kept right up with Ronon the entire time, unlike John who lagged behind most of the time.

When they had left an out of breath John, they had walked back to their respective rooms together, although in silence, when Sophie turned to her door Ronon's low voice sounded behind her.

"You know…you were really good. I mean you kept up no trouble. I'm impressed."

To this Sophie smiled and said.

"Thanks I enjoyed it. I would like to come with you again so if you don't mind me tagging along just say when you're going."

Ronon gave a small smile and answered

"Sure, you're welcome any time!"

He then disappeared into his room.

The opening of the door to the infirmary opening snapped Sophie out of her thoughts, her thoughts being of how she enjoyed the company of Ronon. Through the door Sheppard was helping an angry and injured Ronon into the infirmary. Sophie jumped up and helped Sheppard get Ronon on a bed. All the while Ronon grumbled that he was fine and didn't need any medical attention.

"What happened? I thought you were off-world…were you attacked?" Sophie asked curiously, addressing Colonel Sheppard.

"We weren't made quite as welcome as we would have liked. When we were escaping from our lovely jail cell Ronon took a few hits." This caused Ronon to grunt in annoyance.

"Well I want to see the rest of your team in here when you have some time ok?"

"Sure thing Doc!" Called Sheppard who on his way out added to Ronon "Behave yourself Ronon, I wouldn't want to upset her she's got skills to match yours"

With that Sheppard left.

"Okay, let's take a look at you then." Sophie said as she turned to Ronon. On observing him she noticed blood on his right arm and left leg.

"Ronon, would you mind taking your shirt off please?"

"I really am o…"

He began to say, until Sophie cut him off with a look that stated simply 'Do what I say, or else.' This managed to silence him, and without another word he took off his shirt.

Sophie had to stifle a gasp, he was… well hot! No wait better than that he was…CONCENTRATE! She shook her head and glanced at him to see if he had noticed her staring, luckily he wasn't looking.

Sophie turned her attention to his arm right, just below the shoulder there was a deep gash. As Sophie examined the injury she noticed that the wound looked like it had, at one point, a weapon of some sort lodged in it. It probably had been some kind of throwing star.

"Ronon it looks like this wound was made by the sort of weapon that is thrown. Am I right?"

"Yeah it was like a star thing."

Furious she looked him straight in his dark eyes and said,

"Are you telling me you removed it? Before I got a chance to look at it? Do you realize how dangerous that is, if it had struck you in a major artery and you just removed you could have bled to death!"

All Ronon did was shrug, Sophie felt a wave of anger bubble up inside her.

"If you do that again I will inform Colonel Carter that you will be unable to go off-world, until you can prove that you have some respect for yourself. If you don't I for one certainly won't be treating you!"

"Well I shall leave then."

Ronon began to stand on his good leg, when Sophie's strong arm pushed him back down on the bed and this time it was her turn to growl.

"Stay there! That arm needs stitches!"

Sophie went over to the other side of the infirmary to pick up the stuff that she would need and walked back over to where Ronon was. As she looked at him she wondered 'How could I have been so mad at him? and then felt her cheeks flame as she realized that she was staring at his naked chest, and this time he had noticed. A small smile was playing on his lips.

Blushing even more she prepared an injection to numb the wound ready for it to be stitched up. After it had been injected, while waiting for it to take effect she cleaned the wound.

"So…how come you were the only one injured? I mean no-one else from the team are here so it must have just been you, right?"

Ronon just looked at her and gave her a one shouldered shrug.

The way Ronon reacted gave Sophie the impression he didn't want to discuss it any further. So she left it and prodded the wound to see if it was numb yet.

"Does this hurt? Can you feel anything?"

"Nope it's completely numb."

"Okay I am going to start stitching it up now, so if you can just lay down."

Sophie began stitching the wound up carefully and neatly in silence.

When she had finished she moved to his leg. As she was examining the wound there she grew bored of the silence.

"So…what else do you do when you're not off world, besides going running?"

Ronon smiled slightly and said "I like to spar."

"Is that it, you run and spar? Don't you get bored? I mean isn't there other things you like besides fighting?"

"Nope, Sheppard tried to teach me golf, but it was kinda pointless, you just hit this little ball. I prefer sports that are a little more violent and fun, but I do like films, I have watched many from your world."

Sophie smiled, glad that Ronon was finally opening up to her a little bit more, or at least becoming a bit more talkative.

"Yeah golf is one of our more boring sports. So, do you watch films often?"

Sophie asked as she began cleaning the wound on his leg. It wasn't too bad; it just needed cleaning and a bandage putting on.

"Yeah there are movie nights, but usually McKay sets it up when where here, the team and a few others go, and we watch them together…" Ronon paused for a moment, considering something. "…Would you like to join us we are having one tomorrow night, I mean you don't have to it's just a thought…" Ronon trailed off and looked at Sophie who was stood looking at him with a smile on her face.

"Sure I would love to join you!"

Ronon gave her a warm smile and Sophie felt herself blush again. Sophie attempted to hide it by busying herself with bandaging Ronon's leg.

When she was done she told Ronon he could sit up and then she began explaining to him that staff at the A & E department, where she had once worked, had deemed her riot act. This was because she took it so seriously and if a patient had not listened, well let's just say they only ignored her once.

"So if your stitches bother you at all come and see me. You are ok to train just be careful and if you are in pain stop immediately. Do not just ignore any pain you are in, it's your body telling you it's not ok. Right, take these painkillers and anti-inflammatory pills, and you better take them, ok?"

Sophie ordered as she handed them to Ronon.

. He began protesting straight away saying he was fine and his injuries were nothing. But Sophie was not finished speaking so she just ignored him and continued,

"If I find that you are in anyway ignoring anything I say to you. You will not know what hit you; I'll be so fast on your back. Oh and one last thing tomorrow night just come to my quarters when your going, ok, right any questions?"

Ronon was clearly taken aback with her speech and just shook his head and said that he had no questions.

Ronon stood up, but, Sophie didn't move, they just stood staring into each others eyes.

Ronon and Sophie had been standing there staring at each other for while. If it wasn't for the infirmary door opening and a rather loud McKay walking through it, followed by Teyla and Sheppard, Sophie and Ronon would still be staring at each other. Sophie noticed for the first time how close they had gotten to each other. She felt herself furiously blushing this time, sneaking a glance at Ronon she saw that he was to.

McKay and Sheppard were to busy bickering about whose fault it was the mission had ended so badly, to notice, but Teyla stood in front of them, arms folded with raised eyebrows.

Sophie decided it was best to ignore her questioning look and turned to Ronon and told him he could go. After he had left she told the rest of them to sit on a bed each so she could check each of there health.

By morning she was glad to get out of the infirmary, Sheppard and his team had all left hours ago each with clean bills of health. After they left the infirmary fell silent, this left Sophie to think about her past...

(A/N: Thanks for reading! Hope you still like it, gets a little more interesting in the next chapter. Which will be up asap. PLEASE REVIEW!)


	4. Chapter 4

_**Footsteps echoed all around, Sophie was stood in the middle of the dark room. A room which looked like it was made out of some kind of living materiel. She looked for an escape, as footsteps drew closer. The closer the footsteps got, the more panicked Sophie became, rushing around desperate to escape.**_

_**It was too late.**_

_**The door of her cell opened slowly to reveal her captor. Stood in front of two faceless guards, was the scariest thing she had ever seen. Long, white hair framed the thin face. The face wasn't human; its grotesque features were burning themselves into Sophie's memory.**_

_**The monster began advancing towards her, one arm outstretched and hissing like a snake.**_

_**It was getting closer and closer, even though Sophie was backing up. She had backed straight up into the waiting arms of its guards, who had moved behind her.**_

_**There was nothing she could do. She was trapped.**_

_**The monster's hand touched her chest and Sophie screamed… **_

Sophie awoke with a start, her eyes adjusting to the light in the room, while searching for the noise that had thankfully awoke her from her nightmare. As she sat up in the small bed, Sophie noticed that beads of sweat covered her face and her whole body was shaking.

Sophie jumped as the door chime sounded; glancing at the clock she saw it was it was already six pm. She had slept all day.

Sophie walked to the door in her shorts and a tight fitting tank top, as she opened it she saw who was stood there and immediately wished she had put some more clothes on. Blushing she smiled at Ronon, who had raised an inquisitive eyebrow at her rumpled state.

"Is there something I can help you with Ronon?"

She asked, mentally registering the strained sounds of her own voice.

"Err…I was wanting to know if your coming to watch the film tonight? Because we kinda gotta be there in ten..." Ronon paused as he seemed to notice that she was both sweaty and shaking, "Are you ok?"

Attempting a small smile Sophie replied,

"Yeah sure I'm fine, just err… been out for a run. Yeah that's it just been out for a run"

She smiled broadly and wiped the sweat from her face then continued,

"I'm just so hot after a run. Don't you get hot when you've been running? I mean I do..."

Sophie trailed off as she saw that Ronon's face was one of concern. That meant he wasn't buying her story. She then remembered that she was, in fact, dressed for bed and had the full bed head look going on.

"What's going on, Sophie? Look at you, you're shaking!"

Ronon took a step towards till he was right in front of her, looking down into her dark brown eyes. He put a gentle hand on her shoulder and guided her to her bed where he sat her down and he pulled a chair up in front of her.

"Are you ok?"

Realizing she wasn't going to get anywhere she just said

"I had a bad dream. That's all. It's a lot to take in, all this about Atlantis and the wraith. But I'm fine really. Stay there I'll go get dressed and then we can go watch the film, ok?"

Not waiting for an answer she went into her bathroom and shut the door.

Sophie got dressed at record speed, leaving her long, straight, dark brown hair down after brushing it. After Sophie had gotten dressed she could feel her shakes subsiding. She opened the bathroom door and walked back into were Ronon was sat, his eyes studying her closely.

"Well I'm ready shall we go?" Sophie said smiling.

Ronon just nodded and led the way out into hallway. They walked to Sheppard's room in silence but Sophie could see that Ronon was keeping his eye on her. This was beginning to irritate her by the time they reached Sheppard's quarters.

As they entered his room there was Sheppard, Teyla and McKay and they all greeted Sophie happily, apart from McKay who just looked at her with mistrust. Sophie did not understand his hostility towards her, but just figured he didn't like her because of the self-defense classes. Sophie decided that maybe it was just best to ignore him.

Teyla and Sheppard were sat on Sheppard's bed and McKay on a chair to the right. This left a two seat sofa on the left, which she and Ronon sat on.

While sat there her mind wasn't on Ronon's close proximity, instead however, it was on her dream. Sophie had been plagued by them most of her life. Six months ago however they got worse, not as intense as the one she had back in her quarters though.

Sophie had been nearing the end of her training with only six months to go. The dreams had become worse than ever. Sophie had visited a therapist desperate to get them to go away.

Soon though other cadets in her classes found out and Sophie was bullied constantly. It was a time of her life she was not proud of. Sophie was a strong person with a strong personality, who could usually stand up for herself. However, these dreams brought weakness, and weakness was one thing Sophie could not stand. The therapist offered no help to Sophie, and she became so scared and lonely that within a few weeks Sophie had packed up her stuff and left. The dreams hadn't occurred as often lately and nowhere near the severity of this last.

"You okay?"

The question came from Ronon who was once again looking at her with concern.

She smiled explained that she was fine. Sophie then looked at the screen that had been brought in as McKay started the film, Spiderman. Sophie settled herself into the sofa to watch it, while Sheppard began passing popcorn round. Clearly this was a luxury in Atlantis, one that Sophie was very pleased they had.

About twenty minutes into the film, Sophie was asleep; she had not realized how tired she was, even though she had already slept from the morning till six at night

Sophie had no idea how long she had been asleep, when Ronon had tapped her awake, thankfully waking her from the nightmare with the face descending towards her.

As Sophie opened her eyes she could see the concerned faces of Ronon, Teyla and Sheppard, then there was McKay who looked a little, well, spooked.

Sophie sat up looking around; Teyla was still looking concerned as she asked

"Sophie, are you ok?"

Sophie beginning to get used to lying about this and again just smiled and said

"Sure I'm fine I think I am just really tired, I think I shall go to bed."

Sophie got up off the chair, still aware of everyone staring at her. As she walked to the door Ronon spoke behind her,

"I shall walk back with you"

Sophie turned to say that it wouldn't be necessary but the look on his face showed that he was coming with her whether she liked it or not.

Sophie decided to just accept it and led the way out of the room. They walked back together in silence.

When Sophie was a few metres away from her door, Ronon gently stopped her, by grabbing her arm, and turned her round to face him. Ronon's dark eyes swelled with concern. Sophie tried to meet his eyes, but she couldn't, she felt that if she looked he'd know every secret she held. So Sophie stood staring at a spot on the wall behind Ronon waiting for him to demand to know what was wrong. However it never came, instead Ronon simply said,

"If you ever need someone to talk to, or you need help, you know where I am, Okay?"

Sophie smiled at this, a genuine smile. "Thanks that means a lot…really."

As she said this, Sophie looked into Ronon's eyes. In them she saw something other than concern; however, she was unsure as to what it was; understanding, secrets or even sympathy. Sophie knew that there was something he was hiding.

"Well, you know if there is anything you wish to tell me, feel free."

A small look of confusion briefly crumbled Ronon's expression, before nodding

"Goodnight then Ronon." Said Sophie.

However Sophie did not turn to leave, instead she looked down at her arm were Ronon was still holding it in a grip that was firm but gentle. Ronon also looked down at her arm, where he held her.

Minutes passed as they both just stood there, Ronon looked from Sophie's arm and looked into her eyes, Sophie looked up at him as well, as Ronon moved closer to her. Sophie could have sworn that Ronon was going to kiss her. That was until Sophie's radio activated and Dr Keller's urgent voice filled her ear.

"Dr Wells, this is Keller. Come in."

Sophie jumped back from Ronon and answered,

"Yeah, I'm here. What's up?"

"We have wounded coming in, we need your help in the infirmary."

"Ok I'm on my way"

Giving Ronon an apologetic look she said "there's an emergency in the infirmary I have to go, I'm sorry."

Ronon nodded and said "Go. Don't worry, I understand."

Sophie smiled and ran off in the direction of the infirmary.

It was in the early hours of the morning that Sophie had finally been able to leave the infirmary. One of the teams had come across wraith while exploring a planet. Only one member of the team had serious injuries, the others just needed stitching up.

Dr Keller had spent most of her time operating on the young marine. He had pulled through the operation and Dr Keller was hopeful of a full recovery.

When all the team where settled in for the night Sophie had gone back to her room. As Sophie lay in bed, her thoughts drifted back to Ronon and whether if they had not been interrupted what would have happened.

After tossing and turning for what seemed like an eternity, Sophie finally gave in; she knew that sleep was not going to come. So she decided to go for a walk. Sophie had been wandering in no particular direction for about ten minutes when she came across a balcony, it was in an empty part of the city and the view of the sea from it was amazing. Sophie stood at the railing just observing and thinking.

Her thoughts brought her to home; she hadn't had a proper home since she her mother died when she ten. She still had her father but he was in the air force and wasn't around much. He then died while fighting away somewhere, Sophie was nineteen at the time and she was left completely alone in the world.

At school Sophie was a perfect A grade student, and loved playing sports as well doing Trigonometry. Sophie's mother had always told her she was special, but Sophie just thought that she was different; she had never felt she fit in anywhere.

Atlantis, however, was different; there was something familiar about this place, something Sophie couldn't quite put her finger on.

But why were the dreams back and why were they so bad. A wave of tiredness washed across her.

Sophie moved away from the railing and looked one more time out to the sea, she then turned and went out in to the corridor making her way back to her room.

Upon reaching her room she climbed into bed and almost instantly fell into an uneasy sleep. She dreamed of that face, hissing and coming closer and closer, with an outstretched arm.

( A/N: Sorry it took so long! I have now written chapter 6 and started chapter 7 so I will put them up as soon as my beta's had chance to go over them. I hope you like this! Reviews are very much appreciated!

Also thanks to everyone who has reviewed, added my story to there alerts and added it there favorites. It means a lot! THANK-YOU!!!)


	5. Chapter 5

Sophie awoke with a start the next morning. As she sat up she noticed that she was sweaty from her nightmare again.

She looked at the clock it was half eight, that she was not going to get anymore sleep so she got up and had a shower before getting dressed.

Sophie looked at herself in her bathroom mirror, her eyes were dim, and her skin was unnaturally pale. She looked deprived of sleep but strangely enough she had slept. So she made herself like as best she could before giving up and heading out.

Sophie had nothing to do today, she wasn't needed in the infirmary and she had no lessons to teach, she decided to go to the gym for a bit and then explore the city.

But first breakfast, Sophie had found that if she skipped meals like yesterday when she had hardly eaten anything, she suffered the next day, and so first stop was the mess hall.

When she arrived at the mess hall she waited in line grabbing an assortment of breakfast items before finding an empty table to sit at. She wasn't in a socializing mood today.

Sophie had only been sat there for a few minutes when she noticed Teyla, Ronon and Sheppard enter. Upon seeing them she ducked her head down and concentrated on eating, all the time hoping that they wouldn't see her.

Too late Teyla was coming over with her tray while the others sat at a different table.

"Good Morning Sophie!" said Teyla as she sat down opposite her.

Sophie smiled and said "Hi Teyla."

Teyla studied Sophie carefully for a moment then opened her mouth to speak

"Oh! Look at the time. I have to go, sorry Teyla, I shall see you later"

Before Teyla could say anything, Sophie picked up her tray and left the mess hall.

Whew! that was a close one thought Sophie. She hadn't meant to be rude but she just didn't want to be asked questions or studied closely, even though she knew Teyla meant well.

Sophie headed straight for her room where she changed for the gym, she needed a release and a punch bag was going to be the best she could do.

Half an hour later Sophie was releasing all her stresses by beating the crap out of a punch bag; lines of sweat were breaking out across her forehead as she refused to let up on her punch bag victim.

The doors to the gym opened, but Sophie was in her zone and she did not notice the newcomer.

"What did the bag do to you to deserve this beating?"

Sophie swung round swiping the newcomer's legs from underneath them, with a well placed kick. Instantly she regretted it as she saw Ronon sprawled out on the mats. Sophie rushed to his side already apologizing profusely.

"Oh my god! I'm so sorry I didn't hear you come in, you scared me. I really am sorry. Are you ok?"

Ronon gave a small laugh and said "Sorry it's a habit, the quietness that is."

A sudden realization dawned on Sophie,

"Your leg! Oh my god I kicked you and you have a bad leg. Here let me take a look."

With out giving him a chance to argue she had rolled the bottom of his trousers up and was checking over the wound, after a minute or two, she said,

"It looks ok, it's healing well."

Sophie got up and offered Ronon her hand which he took so she helped him get up.

"Mind if I join you? We could fight again if you want?" asked Ronon cautiously.

Sophie liked the idea of fighting a real opponent, but Ronon was still hurt, so she hesitated glancing at his leg.

Ronon followed her gaze and said "I'm fine, really."

Sophie smiled and said "let's fight"

They both took up their respective stances and began fighting. It started off with the same ferocity as last time, but after they had both won a couple each, Sophie felt her concentration slip. This earned her a hard slam back into reality as Ronon cleanly laid her out across the floor, without even giving her a chance to block him or fight back.

Winded Sophie lay there gasping for breath. Ronon crouched next to her.

"You're not concentrating. I am not fighting you again until you tell me what went on yesterday when you opened your door you looked truly terrified. Then later you fell asleep in Sheppard's room and start screaming in your sleep. Just tell me what it is…Please."

Sophie got up and walked over to the window at the other side of the room, facing away from Ronon and looking at the sea below, she felt she had no choice.

"My mum died when I was ten, after her death the dreams began. They weren't that bad just a dream, but they were constant, most nights I would have them. They did eventually stop but then my dad died when I was nineteen and they started again. But, again they stopped after a while, six months ago however they came back. I was in the last six months of training for the Air Force. They got bad, very bad. It got that I was scared to sleep… I went to a counselor thinking they might be able to help. They didn't. Nothing they said helped at all. My classmates found out, I don't know how but, it gave them a reason to start at me…"

Sophie paused trying to keep her composure. She heard Ronon move closer to her, he lightly rested a supportive hand on her shoulder, Sophie continued barely holding on to her composure.

"…They bullied me, and I let them. For the first time in my life I wasn't in control. I left, I couldn't take it anymore. I packed my bags and I gave up, all because of these stupid dreams that aren't even real."

Sophie could feel Ronon's eyes on her as he asked "These dreams, what are they about?"

Sophie laughed a dry, humorless laugh

"It's stupid, I'm trapped in this room and this thing comes in, its grotesque and it just walks towards me then two of its guard things grab either side of me. It's really not that bad, but, for some reason it terrifies me…"

Sophie finds herself unable to carry on and Ronon pulls her towards him and envelopes her in to a protective embrace.

They stand like that for some time, before the city's intercom interrupts them.

"Sophie Wells please report to my office, thank you!"

Sophie looked up at the speakers, where Colonel Carter's voice had come from and sighed slightly. She didn't want to go, she felt safe in Ronon's arms. Sophie, however, knew that she must move, so she pulled away from Ronon, regaining her composure. Ronon looked down at her and smiled reassuringly.

"Thank you for listening Ronon. It meant a lot. Don't worry though I'm fine, I'm not crazy or anything… I suppose, I err…better go then."

Ronon just nodded.

Sophie left the gym feeling like a huge weight had been lifted off her.

When Sophie arrived at Colonel Carter's office she could see Doctor Keller, and Colonels Carter and Sheppard. It looked like they were having an urgent discussion. Doctor Keller was saying that there is something not right in some test results. To which Colonel Sheppard exasperatedly said "then run more tests!" Sophie was unsure as to whether she should interrupt or just wait. However Sophie was relieved when Colonel Carter noticed her and abruptly ended the conversation then waved Sophie in.

Sophie walked in and instantly she could feel the tension in the room, making her feel uncomfortable.

"Sophie I have been speaking with Colonel Sheppard and Dr Keller and we have something to propose to you. John here tells me you are excellent in combat and Jennifer tells me you're a good doctor. Right now we are lacking a field medic with defense skills and some military training. You have all the necessary requirements; we want you to assist mostly John's team off world as well as other teams if needed. It will generally be in a medical capacity but you may need to you use your skills for other reasons. So will you do this?"

Sophie stood there; she had been taken completely off guard.

"Err…I really wasn't err…well. You know what sure I'll do it, yeah, count me in!"

Colonel Sheppard spoke next "Right well we are going on a trade mission tomorrow, it should be simple. So you can come with us and get a feel of what it's like going off world."

"Yeah, sure, sounds great!"

A few minutes later Sophie left the office with her instructions for tomorrow. She was excited, but, she also got the feeling there was something else, something that she wasn't being told.

Walking back to her quarters she saw Ronon and told him that she would be joining him off world tomorrow. He smiled and said "you know anytime you need to talk again, I'm here"

Sophie smiled at this and hugged him, before continuing back to her quarters.

(A/N: As always I hope you enjoyed this! I started to explain Sophie's background here, but in the next few chaps we discover that there's a lot more to it. Please review! And Thanks to everyone who reads!)


	6. Chapter 6

Chapter 6

The next morning Sophie got up and was in the mess by half six. Today she was going on an off world mission. Her first. Sophie was surprised when she arrived in the mess hall to find Sheppard and his team already sat there. Ronon looked up and gave a smile when he saw Sophie, this caused the others at the table to look over towards Sophie. Sophie smiled and walked over to them with her tray, she pointed to the empty seat next to Ronon and said

"Mind if I join you?"

Colonel Sheppard was the one that answered,

"Sure, join us! So, you excited about going off world for the first time?"

Sophie smiled like a little child who had candy dangling in front of her face,

"Yeah! I'm sooo…excited!"

This excited outburst from Sophie caused the rest of the table to laugh, apart from McKay, who just turned away from her and carried on eating.

When Sophie raised her eyebrows at this Sheppard looked at McKay and then to Sophie and said

"He just got out of the wrong side of the bed this morning."

Sophie turned back to her own food and muttered "Seems like that everyday to me."

"Excuse me! Do you have a problem?"

Sophie looked up from her food to see McKay glaring at her over his own food. Sophie was getting fed up with McKay's attitude towards her ever since she got here. McKay constantly stared at her as if waiting for her pull a gun out and shoot people or he'd just pass comments.

"No I don't, but you clearly do! Ever since I got here you either just stare at me as if constantly keeping me in check or you have these snide remarks. So clearly it is you who has the problem and I quite honestly want to know what it is! What makes you think that I'm not worthy enough to be on your precious Atlantis?"

Sophie was very angry at this pointed shouted the last part, causing the entire mess hall; which was quite busy, to collapse into silence and all look at her.

Sheppard just put his head in his hands and Teyla looked shocked. It was Ronon who spoke next.

"McKay, just because you're jealous doesn't mean you have to act like such an ass" growled Ronon.

Sophie confused looked around the table before saying,

"Jealous of what?"

Briefly she saw worry cross both Sheppard's and McKay's faces before they both set into a neutral expression. It was Teyla who interrupted her thoughts.

"Sophie, McKay is jealous of how well you have integrated into Atlantis and I am sure he is also ashamed of himself for the way he reacted, aren't you Rodney?"

Teyla locked Rodney with a piercing glare. This told Sophie all she needed to know, there was something she was not being told. This was confirmed when she looked at Ronon, he sat there more rigid than normal, a look of unease on his face.

Sophie smiled and said to McKay

"I'm sorry McKay if I have caused you problems. I just hope that we can be friends. Now I am going to go get ready, I shall see you in the gate room later.

Sophie then got up and left, feeling the gazes of everyone in the room on her back.

By the time Sophie met Sheppard and his team in the gate room she had already decided that she going to find out what was going on. She also knew exactly how she going to do it. When she had left the mess hall two hours earlier she had gone straight to the infirmary where she pulled her medical records out. The last page showed the results of a blood test, there was something there that shouldn't have been. Sophie was well aware of the ATA gene, but this was something different and was a prominent feature in her blood. Sophie took that last sheet and placed it in her vest pocket.

The gate started up when she joined Johns team. Teyla smiled at her "You ready?"

Sophie smiled and nodded. Sheppard turned to Ronon and said "your in charge of Dr Wells" he then turned to Sophie. "Sophie stay with Ronon."

With that the team moved thought the gate.

Upon reaching the other side Sophie had to gasp; the entire village about half a mile from them. was destroyed and there were only a few houses remaining. A hand grabbed Sophie's arm in a firm grip, she looked to see Ronon's hand there, and Ronon was just staring out at the view in front, expression blank. Teyla's expression showed grief and anger, whereas Rodney looked sick. It was John, who pulled the team back together though by saying,

"Let's check for survivors."

The team moved out with a sense of urgency and sadness throughout them. The whole walk there Ronon kept hold of Sophie's arm. Sophie decided not to say anything to him; she just let herself be guided.

"Was…was it the Wraith?" Sophie asked cautiously as she stood in what must have been the town square. The place was decimated and there was an eerie chill about the place that put Sophie on her guard even more.

"Yeah… they took everyone. There's no-one left." Growled Ronon.

Nobody else spoke as they walked through the town searching through for survivors. Sophie got the impression that the team knew there weren't going to be any, but they felt they had to try.

Hours later after being unsuccessful in the town Teyla suggested that they should try the nearby caves. The five of them feeling even less hopeful, decided to give it one last shot before leaving this world behind.

Just as the caves came into site, Sophie noticed Teyla stop walking, Sophie turned to her and was about to ask her if she was ok when Sheppard walked over,

"Teyla...What is it?"

Teyla seemed to snap out of her trance like state and answered Sheppard conveying true disgust in her voice.

"Wraith!"

Within seconds of hearing this Sheppard yelled for everyone to get back to the gate.

But it was too late.

Ronon heard it first and he looked up, a wraith dart. Sophie followed his gaze and saw the small aircraft heading towards them.

Somebody yelled, "Get into the caves!"

But before she could acknowledge who, someone grabbed her arm and pulled her.

She turned to see Ronon was the one dragging her along and the others just in front. Reality set in and Sophie's legs took over as she began running on her own.

She was only a few metres from the cave and she started thinking she was going to make it. Suddenly, a solid body smacked into her side and she was knocked out of the way of the beam that the dart had used. But as soon as she hit the floor she was pulled up again and dragged the remaining metres into the safety of the cave.

She turned to Ronon "Ronon thank you, you saved my life!"

Ronon just nodded and turned to Sheppard and said

"We need to get out of here!"

Teyla joined Ronon and Sheppard and said

"If we leave now, we will be caught. I believe our best option will be to wait till nightfall. I believe that will give us the best chance."

"Yeah Teyla's right. Ok… this cave doesn't go anywhere so that means there is only one entrance and exit. We can take it in turns at keeping watch. I'll take first watch."

John then moved to the front of the cave, while Sophie and the others moved towards the back.

Sophie glanced around, the cave was dark but she could still see clearly. The rest of the team sat separately apart from Teyla who came and sat next to Sophie.

"Are you ok?" she asked. When all Sophie did was shrug, Teyla said "Nobody deserves that; they couldn't even try to save themselves. There would have been nothing we could have done, there would have been too many Wraith."

"Yeah, it's just hard…" Sophie's thoughts drifted.

Sophie reached into her vest pocket and pulled a piece of paper out of it. She began reading through, it for what seemed like the hundredth time, when a hand grabbed the paper out of her hands, an irritated McKay who was between Sophie and the paper demanded,

"Where did you get this?"

Sophie looked at McKay and simply said

"My medical record."

"Well…you…well…you…shouldn't have that!" McKay practically yelled. Causing Sheppard to turn round and ask "What the hell is going on?" he then walked towards them, signaling Ronon to cover the entrance. The expression on Johns face showed he was angry.

"Yeah I think I have the right to have my own medical record. Unless there is something on it that I'm not supposed to see."

Sophie looked around and saw everyone's faces. She was right. There was something going on that she didn't know about.

But what were they hiding from her?

(I hope you enjoyed this! I will not leave you waiting long for the next chap, I just have some editing to do to the next one. It will be up very soon!

Thanks for the reviews of the previous chapter I appreciate it.

Please Review! and Enjoy!)


	7. Chapter 7

Chapter 7

She felt herself snap. The last few weeks on Atlantis had been fun, but she had this nagging feeling that something wasn't right. However, she felt so at home on Atlantis.

"McKay you've got a problem with me and it has something to do with that paper in your hands. I am not asking anymore, you tell me what it is, or I swear I'll…"

Both Sheppard and Teyla stepped in between Sophie and McKay,

"Why don't we all calm down and talk about this rationally" Teyla said trying to reason with both Sophie and McKay.

Sophie, however, was angry and was not ready to back down; instead she turned to Teyla and said,

"So do you know? Are you gonna tell me?"

She faced Sheppard next,

"Colonel will it be you? I am telling you right now I WANT TO KNOWWHAT IT IS!"

Ronon turned from the cave entrance to face them and said to Sheppard,

"I told you it wasn't fair doing this! I think you should tell her…everything, OR I will."

This from Ronon would have made Sophie smile if she wasn't already so angry.

Sheppard sighed and said,

"He's right, you deserve to know."

He glanced at McKay before continuing

"Sophie, you weren't brought to Atlantis to teach self defence. Well that wasn't the main reason anyway. The thing is, your blood shows you have the ATA gene. Which means you can use Atlantian technology. However, yours is much stronger than anybody else's. There is another thing… your blood also possesses something else, something that we haven't identified yet. All we know is it shouldn't be there."

"WHAT! Does…does that mean…I'm not human?"

Sheppard opened his mouth to answer but Teyla got there first,

"Sophie you are human, you possess the same qualities of any human both physically and mentally. We just don't know what this other thing is."

Sheppard joined back in the conversation

"This thing in your blood was picked up when you were training at the air force academy and one of their doctors contacted the SGC. You were assigned here so that we could try and work out what it is; for all we know it could be nothing, maybe a kind of by-product of the gene. We just haven't ever seen it before."

Sophie's anger dissipated and fear grew inside her. Her mind was racing. Was she normal? Was there something wrong with her?

Sheppard suggested, "look lets just get out of here and then we will discuss this back at Atlantis."

Sophie just nodded while staring at a spot on the wall, there were so many things going through her head that she couldn't think straight.

That's why she went to Ronon and offered to join from him for a bit. He had smiled slightly and nodded for her to sit down. Sophie looked at Ronon,

"Did you know?"

Ronon, still staring out into the forest, nodded before turning back to her and saying,

"I wanted to tell you, but you were having those dreams and I didn't want to make them worse."

Sophie nodded and said "I would rather have been told though….but I " She trailed off as Ronon hand reached up and tilted her chin up so she was looking straight into her eyes. They were close enough that she could feel his breath gently stroking her cheek.

A wraith stunner was shot from the forest narrowly missing them both. Both Sophie and Ronon immediately took cover in the entrance of the cave, pulling out there weapons.

The rest of the team joined them seconds later with their weapons also raised.

Sheppard looked at Ronon and asked "how many?"

Ronon shrugged "There could be one or one hundred"

"I do not sense many, perhaps ten, but not many more."

"Right, plan is we take them. Then we run for the gate, its nearly dark, this may be our best and only chance. Ronon, stay with Sophie. Do not let her out of your sight."

Slowly, the team began moving out of the caves. They had got only approximately one hundred metres away from the caves when a shot from a wraith stunner narrowly missed Sheppard. The entire team stopped, each member scanning the area for the owner of the weapon.

SNAP!

Ronon and Sophie turned to were the sound came from, both had their weapons raised. Sophie turned and came face to face with a wraith. Frozen with fear, unable to get herself to move, she had no chance to defend herself from the blow when it came. A blow that took Sophie off her feet and flying to the floor, the metallic taste of blood filled Sophie's mouth as she sat up from her place on the floor with the help of Teyla. Sophie sat up in time to see her wraith attacker slump to the floor, dead.

Sophie scrambled up trying to put as much distance between herself and that thing as possible.

"Sophie! Its ok, it's dead." Called Teyla as Sophie continued increasing her distance. She continued backing up until she back into the strong body of Ronon. Who grabbed her by the shoulders and turned her around to face him she could the concern in his eyes and she knew he could see her pure terror in her own.

Sophie, however, was thinking straight, she needed to get away from them all. They had lied to her she couldn't trust them anymore. She needed to go. To figure this out for herself, she needed to shut everyone else out. Again.

Pulling away from Ronon, Sophie lost all control, Ronon tried to keep hold of her but she shoved him away and ran.

It was while Sophie was running listening to the voices calling after her, that she thought 'why am I running?' Sophie slowed, she knew she was panicking.

Moments later Sophie stopped and turned to face the people who were trying to catch up with her. Her team.

She turned expecting relieved looks, instead however the looks she received where ones of horror.

A split second later the full team was yelling for her to run and pointing behind her.

Sophie's stomach dropped and she turned, only to be dissolved in a light.

The rest of the team staring at the spot she had stood, moments earlier.

(A:N I hope you enjoy this I can't promise another quick update but I will try!

But please do review!!! Thanks for reading!)


	8. Chapter 8

Chapter 8

Chapter 8

(A/N: Ok I am soooo sorry for the long wait especially on a cliff hanger! But I have two more updates coming for you guys very soon!

I have to say a massive Thank-you to journeyman07 for the help it really helped!

I hope you all enjoy this and reviews are appreciated so much!!)

When Sophie opened her eyes, the first thing she noticed was that she wasn't on Atlantis. The last thing she could remember was running. She remembered running and then stopping, turning towards the others and their faces showing only horror.

Sophie couldn't get their faces out of her mind.

Sitting up slowly, Sophie looked around the room, trying to work out where she was. She was in a cell, but something felt familiar about this place, yet she couldn't work out why. The sound of approaching footsteps caused Sophie to stand up. A wave of dizziness crossed her causing her to reach out and grab something to steady herself. When she opened her eyes again, she saw she was holding the net-like bars to her cell. On the other side was the monster. The Wraith.

It all came flooding back to Sophie. She had run because the monster that had attacked her was like the one out of her nightmare. It was a Wraith that was haunting her sleep. Sophie however was still confused because today was the first time she had seen a wraith, therefore how could she have experienced the dreams about them before she even knew they existed let alone met one?

Sophie looked at the wraith. It was disgusting, just like in her dream. Quickly, she removed her hand from the front of her cell and backed up against the far wall, putting as much distance as possible between her and the wraith. She looked down at her hands and she could see them shaking. She knew her whole body was shaking and she knew it was with fear.

At either side of the wraith there were two of guards with masks covering their faces. The wraith signaled to these guards and they opened her cell, moving forward to grab her. Sophie pushed herself as far into the wall as she could and tried to push the advancing guards away. She kicked one, causing it to stumble and as she turned towards the other she received sharp blow across her face. She fell heavily to the wall. While she was still disorientated, the guards grabbed each of her arms and dragged her off.

Sophie hoped that the others didn't get captured as well, or worse killed. Scolding herself, she pushed that thought to the back of her mind and instead concentrated on the thought of rescue.

The wraith led the way throughout the whole journey and when they went into a room she saw it bow down in front of something. Sophie looked up to where he was looking and she saw a large grotesque throne chair. Its occupant, however, was nothing less than grotesque.

It was a female, a queen. Sophie remembered reading mission reports about the queens. They were powerful, more powerful than the males. Their telepathy was stronger and could cause people to hallucinate. Yet it was the sheer view of her that struck Sophie with the most fear. She was truly terrifying.

The queen beckoned the guards to bring her forward; Sophie tried to fight it. She really didn't want to get any closer to that thing. As she managed to get away from one of the guards, a blow to her ribs sent her reeling back into its hold. Wincing in pain, she looked for the source of the blow. She could see that it came from the back end of a wraith stunner, which was now being held by the male wraith.

"Bring her to me." the queen's eerie voice ordered.

The guards complied but this time kept a tighter hold of Sophie's arms. Arms that were getting sore from where they were holding her and she was sure she had a few broken ribs. She was dragged until she was only a meter away from the queen - who smiled at Sophie. It was a smile that crushed any sense of hope that Sophie was trying to hold onto.

The next thing Sophie felt was the searing pain of the queen entering her mind and filtering through her thoughts and memories, taking what she needed. Sophie closed her eyes trying to block her out, but she was too strong,

"What a boring mind you have."

The queen's voice echoed through Sophie's head as she explored the darkest corners of her mind.

"Ahh!…What's this then?"

Just as Sophie thought she couldn't take any more the pain lessened in intensity, the queen had left her min. As Sophie opened her eyes, she saw that once again the queen was smiling.

"Hmmm…you're different. Your friends knew that and they didn't tell you. That hurt you didn't it. They think you're a monster, don't they?"

Sophie felt tears well up in her eyes even though she knew the queen was trying to get into her mind, trying to get a reaction from her, she just couldn't pretend that she didn't think that. Why hadn't they told her? Were they scared of her? Another part of her brain however tried to reason with this by saying 'If they didn't trust you then why did take you off-world with them?' unless it was a test to see were her allegiances were.

Sophie shook her head and said with tears freely flowing down her cheeks

"I AM NOT A MONSTER!" Sophie cried.

"Oh but you are! You are more like us than you can imagine!" hissed the queen.

Sophie stared at the queen wide eyed, could it be true was she more wraith than human? Panic was setting in and Sophie felt herself begin to shake.

She didn't even hear the queen order them to take her away, her mind was racing so fast. She couldn't hear anything other than her own thoughts pounding through her brain.

The next thing Sophie knew she was being thrown into a room. She cast a brief glance around that was only good enough to ascertain that she wasn't back in her cell but in a different room, a strangely familiar room.

The door shut behind her and she was left alone. Sophie walked to the far wall and sat down leaning against it. With her head in her hands Sophie closed her eyes.

When she arrived on Atlantis she had immediately known there was something different. For the first time in her life she had a home: Atlantis. She had made friends easily, especially with Colonel Sheppard's team, well, except for McKay, he had seemed suspicious of her at first and things had only deteriorated from there. Now she knew why.

The Queen had said she was like the wraith, was it true?

Maybe it was for the best she had been captured if she had stayed on Atlantis she could have put the entire expedition in danger. At least now she could no longer pose a threat to them.

Sophie woke with a start. She was lying against the wall at the back of the room and had no idea how long she had been asleep.

Sophie slowly stood up feeling the pain in her ribs. The room was dark and she walked towards the middle and looked around.

She gasped.

This room was the room from her dream.

Seconds later the sound of approaching footsteps filled her ears. Her dream, it was true. All along she had maintained that it was just a dream and it wasn't real.

All along she had been wrong.

The footsteps grew closer and Sophie desperately searched the room for an escape or at least a weapon. Too soon the doors opened and the wraith stood there before her. Sophie backed up, straight into the arms of the guards who had moved round her unnoticed. The wraith outstretched its hand and began moving towards her.

This was it, thought Sophie, this was were she died. Her dreams tried to warn her but she didn't listen to them.

The wraith hissed; it was only a meter away from her now. Sophie tried to escape, but the guards held on tight. The wraith stepped closer its hand only inches away from her chest.

Sophie squeezed her eyes shut determined not to see the pleasure on the wraith's face as it fed from her. She felt its hand touch her and instantly felt pain - she screamed. Sophie expected the pain to worsen, but it didn't. The hand fell away from her chest. Sophie opened her eyes to see the wraith fall to the wall.


	9. Chapter 9

Chapter 9

Sophie looked behind the wraith from where it had been shot. In the doorway to the room stood Ronon and Sheppard. Sophie looked at the guards on her arms. They let go simultaneously, reaching for their stunners. However, before they could fire a single shot, Sheppard and Ronon opened up with their own weapons. The guards hit the ground and Sophie went down with them, no longer able to support her own weight.

Ronon rushed towards her while Sheppard covered the door.

"Are you ok? We need to get you out of here!" said Ronon, concern evident in his voice.

"No! You cant you have to leave me. I'm too dangerous for you to have around." Sophie said quickly.

Sheppard looked at her from his position at the door "What are you talking about?"

"The Queen she said I was like them, more like them than I knew."

Ronon growled "You are nothing like them!"

Sophie tried to pull away as Ronon reached down and grabbed her by her waist and hauled her onto her unsteady feet. His grip was strong and before she knew it he was practically carrying her down through the hallways of the hive.

Sophie began feeling dizzy and light headed after walking only a couple of hundred meters. She knew she was leaning heavily on Ronon, but she could also see that he wasn't struggling with her.

After rounding one corner Sophie felt herself being quickly dragged back round into cover away from the wraith stun blasts that had shot past them. Ronon left Sophie lent against a wall while he and Sheppard fought the wraith.

The longer she walked with Ronon, the hazier her sight became. Sophie couldn't remember when but she noticed Sheppard was supporting her other side as well.

Eventually they came to a large open area. Glancing around Sophie could see darts everywhere. Then the back of a puddle-jumper materialized in front of her and the faces of Teyla and McKay came into view as the ramp opened.

Sophie didn't even hear their greetings to her. She felt herself being lifted up and placed on to the seats in the back of the jumper. Something soft was placed under head and Teyla's face filled her hazy vision.

"Sophie, we will be arriving at the Daedalus soon. You are safe."

Sophie gave a small smile at this and saw Ronon next to Teyla. She reached out and took Ronon's hand before letting her eyes close and allowing sleep to take her.

When Sophie woke she didn't open her eyes straight away. Beep, beep, beep. She opened her eyes to look for the source of the annoying noise, which was the machine next to her monitoring her vitals. She looked round, things still a bit blurry but she could tell she was in Atlantis' infirmary.

Coming from the other side of the room, she could see someone walking towards her. It was Dr Keller; she had a smile on her face.

"Sophie, I'm glad to see you awake," said Keller with a smile, before checking the machines around Sophie, "How are you feeling?"

"Bad headache," rasped Sophie.

Dr Keller smiled and nodded then turned to a nearby nurse and asked her to bring some pain medication.

Sophie didn't see the medication being administered, because, she fell asleep again moments later.

This time when Sophie woke again she felt much more alert and her headache wasn't as bad. A nurse came over when she saw Sophie was awake. The nurse checked her vitals and asked her how she was feeling. Satisfied with Sophie saying she felt much better, she went away again.

For what seemed like forever Sophie lay there going over the past few day's events again and again. She soon grew bored and tried to sit up in her bed but she moved too quickly and jolted her ribs, which she noticed had been heavily bandaged. Next she unsuccessfully struggled to get sit up for five minutes before she saw Dr Keller and Colonels Carter and Sheppard enter the infirmary and walk over to her. Dr Keller hurried to her side and helped her get settled before saying,

"You have several cracked ribs, you shouldn't be moving around."

Sophie just nodded her agreement to this and looked at the two Colonels stood at the foot of her bed.

"Sophie, how are you feeling?" Colonel Carter asked politely.

Giving a small smile Sophie said, "Better, the headaches not as bad now."

Colonel Carter nodded and continued, "I was wondering if you were feeling up to talking about what happened and then there are a few things we should explain to you."

"Sure."

All three visitors pulled up chairs and sat at Sophie's bedside waiting for her to begin.

"Well, before I came to Atlantis and especially during my military training I suffered from these nightmares. They continued on for a long time and people started well bullying me. I hated feeling so weak so I just left. The dreams continued but they weren't as often and nowhere near as bad. In away I grew accustomed to them and they didn't bother me as much." Sophie paused and she received a reassuring smile from Carter, so she continued.

"When I came to Atlantis it straight away felt like home…"

"Trust me that's common here," said Sheppard from his chair.

"No, this was different. I felt I belonged here and that's something I've never felt before. Then the nightmares got worse. They started to happen every night and the intensity of them…they were horrible."

"What was the dream about?" asked Keller.

"It was this monster walking towards while two of its guards pinned my arms. Its arm outstretched with a face that..."

Sheppard sat up in his chair, "Wraith. Your dream, the monster was a wraith."

Sophie nodded looking down at the bed in front of her.

Colonel Carter looked confused, "wait you said you had these dreams before you came to Atlantis, but you didn't even know the wraith existed and you only ever saw one for the first time the other day. That doesn't make sense."

Looking up Sophie shook her head, "I don't understand it either, but…but…when I was on the hive ship I was taken to the Queen. She looked into my mind, the pain was unbearable, but she said things. She said…I was different, that I was more like her than I knew."

Tears welled up in Sophie's eyes and she struggled to keep composure.

Dr Keller reached over and took her hand, and began speaking gently to Sophie, "You are nothing like them. Your blood does have something different in it though, and I may not have identified it yet, but I can promise you that it is nothing like Wraith DNA. Now when you're up and about we can work on it together."

Sophie gave a small smile and turned to Sheppard and said, "Thank you for coming to rescue me, I am curious though how did you get there?"

"Hey don't worry about; it was a piece of cake, wraith cake. We knew there must have been a hive in orbit, so we escaped back to Atlantis, got in a jumper and gated to a nearby planet and snuck aboard the hive. Meanwhile Atlantis contacted Daedalus and rerouted it. They kept far enough away staying out of sensor range of the hive but close enough to pick us up when we had you. See easy," he said smiling reassuringly.

"You need to rest Sophie, don't worry, we'll figure out were your dreams came from and what's in your blood when you're better." Said Keller, who squeezed Sophie's hand and stood up and then headed over to her office.

"See you later Sophie and don't worry." Smiled Carter and she left the infirmary.

Leaving Sophie with just Colonel Sheppard.

"Colonel... I'm sorry. I should have never run off, I risked all everyone's lives, I just freaked."

"Sophie, I understand and don't worry about it. You will still be part of my team when we need you, wont you?"

Sophie smiled and nodded.

"Good, now rest! I will come back and see you later." With that Sheppard left.

Sophie took a few moments to get as comfy as possible before going off back to sleep.

This time when Sophie woke up she could see Teyla and a nervous McKay, sitting at the side of her bed.

Teyla smiled when she saw Sophie was awake.

"Sophie, how are you feeling?"

"Better" replied Sophie.

"I'm very pleased that you are, Rodney has something to say you, don't you Rodney?"

Slightly startled, McKay looked from the spot he had been staring at on the far wall and looked from Teyla to Sophie.

"Yeah I…err wanted to apologize. I haven't been very welcoming and well I guess that it's I really am sorry, maybe we could be friends and start again."

Sophie smiled widely at this, "sure thing, McKay and apology accepted."

McKay gave a little smile then started going on about some experiment and hurried out of the infirmary.

Sophie watched him leave then turned to Teyla who spoke as Sophie opened her mouth

"I did not ask him to do that, it came from him. He did not want to do it alone. I think he is a little scared of you."

This made Sophie laugh, but she soon stopped when she jarred her ribs.

"Ronon has been worried for you. He sat by your bed ever since rescuing you, until that is Doctor Keller kicked him out for his own health." Teyla let this information sink in and Sophie couldn't help but smile at this, Teyla continued.

"In a few minutes there's a briefing, I thought you should know John and Colonel Carter will be explaining to me, McKay, Ronon and some other personnel what you explained to them."

Sophie nodded, "thanks for telling me. I really just need some answers now."

Teyla stood up to leave but stopped she reached and picked something up it was a file.

"Colonel Carter gave me this, its all about the ancients, including things about the ATA gene. She said it might help."

Teyla passed her the folder, said she would see her later and left, leaving Sophie to happily read through her file.

_**She walked down the hallway of the house, the house she used to call home. She walked into the bedroom with the bream walls and flowery curtains and bedding. Laid in the bed was a beautiful woman, she was asleep and looked completely at peace. The woman was her mother; Sophie felt tears well up in her eyes at the sight of her mother dying.**_

_**The door opened behind her and Sophie's dad walked in and ushered Sophie out of the room.**_

_**As the door shut behind her, Sophie looked around suddenly it was night, Sophie walked slowly towards the door to her mothers room again. Carefully pushing it open slightly, she was blinded by a flash of light that rose from her mother's bed.**_

(A/N: I have to thank-you so much for reading!

I hope you like it!

I have one more chap wrote so if anyone has anything they really want to see in this let me know, although this maybe easier to do when chapter 10 is up which will be up tonight hopefully!

Again big thanks to journeyman07!

So please take a moment of your time and review, they inspire me!

Thanks)


	10. Chapter 10

Sophie opened her eyes, the dream, it was a memory of when her mom had died

Sophie gasped and instinctively covered her eyes, shielding them from the bright light. When she moved her hands away from her face and opened her eyes she could see that the light was gone, she was laid in the infirmary on Atlantis.

Sophie smiled when she saw the sleeping form of Ronon in a chair next to her bed. As she looked from Ronon, she saw Dr Keller walking over to her,

"Sophie, are you ok? You looked a little spooked when you woke up."

"I'm fine Dr Keller, it was just a dream, well more of a memory from when my mum died. That's all, its nothing really," Sophie said, smiling weakly.

"You wanna talk about it?" Dr Keller said giving her hand a reassuring squeeze.

Sophie shook her head saying, "I'm fine. I'm over it. It was a long time ago. There is something that still bothers me though, the moment she died I remembering seeing this bright white light…"

Sophie looked curiously at Keller she had a strange look on her face, "is there something wrong Jennifer?"

Keller smiled and said, "no nothing, I err… have to go talk to someone, I'll be back later."

With that Doctor Keller left the infirmary.

Sophie sighed and moved carefully adjusting her position on the bed so as to be as comfortable as possible. She then picked up the file from her table and began reading from where she left off.

She had not got very far when she noticed Ronon stirring from his place in his chair. She put her file down and smiled when she saw Ronon looking at her through sleepy eyes. He sat forward in his chair and rested his elbows on the edge of her bed,

"Hi, how are you feeling?" Ronon asked in a soft voice.

Sophie smiled, "good, really good, apart from the ribs that is… So, I'm sorry for all the trouble I caused I…"

Sophie found herself unable to continue.

Ronon was looking straight in to her eyes, "you don't need to apologize, I understand. If you ever need to talk I will always be here for you."

By the time he had finished speaking, Ronon's hand had moved to Sophie's cheek where he gently stroked it before cupping her cheek.

"Dr Wells, I have something!" McKay shouted as he ran into the room. Both Ronon and Sophie quickly pulled away. In doing this Sophie jarred her ribs, causing her to grimace.

McKay however was completely oblivious to the fact that he had interrupted Ronon and Sophie, and was now standing at the foot of Sophie's bed bouncing like a small child from one foot to another. He also didn't noticed Sophie's blush that was growing on her cheeks or Ronon's irritated face, as they both sat staring at him.

"McKay!" It was Ronon who eventually broke the silence. "Are you gonna tell us?"

"Hmm…oh…yes! Of course I'm err just waiting for the others to arrive."

As if on cue the infirmary door opened and John, Teyla and Sam walked in.

"McKay what have you got?" asked Sam curiously.

"Well I can't say just yet I am waiting for confirmation from…"

He stopped talking when Dr Keller walked into the infirmary and made her way straight over with a smile she turned to McKay and said "You were right!"

Sophie felt a little relieved at hearing that they knew what it was but she was terrified that it really was Wraith DNA or something.

"Sophie, you have the ATA gene…"

"Which we already knew" Ronon said testily, growing more irritated and impatient.

"Yes we did thank you, Ronon, for pointing that out!" replied Rodney, his voice drowning in sarcasm, "anyway, as I was saying you have the ATA gene as well as something else. Something that we didn't know what it was, until now…"

"Err…we still don't exactly know what it is…" Keller pointed out.

Rodney turned to Keller "Actually we do!"

"Rodney," scolded Dr Keller "We think we know where its from but we need more information to ascertain what it is."

"I think I speak for everyone when I say this, can you tell us what you do actually know?" Colonel Carter said, her voice thinly layered with the hint of an order, she too was getting irritated with the wait.

"Yes, yes I'm getting to that if people stop interrupting me" McKay spat, glaring at Keller, who just ignored his look, "anyway as I was saying its DNA, specifically Ancient DNA. When we ran it through the database it came up with a match. However the problem is that Sophie's physiology isn't the same as that of an ancient, so she isn't an Ancient."

All heads turned to face Sophie who looked just as shocked as everybody else.

It was Teyla who recovered first, "Rodney, how is it that she posses this…DNA…if she is not one of the ancestors?"

Keller jumped in, "That's the problem, the only way she could possess this is if one of her parents was an ancient, but they all ascended a long time ago…we also don't know what abilities this DNA may or may not give her…"

Sophie didn't hear anymore her mind was in overdrive. Flashes from the past, the strange conversations with her dad and the supposed fear of hospitals her mom had.

It all suddenly clicked into place.

"Oh my god…"

Everyone turned to face her.

John had a concerned look on his face. "Sophie its not that bad…" he began, but Sophie silenced him with her hand as she reached for the file she had been given the night before. The others in the room all looked at each other with confused expressions.

Sophie flicked through the file and stopped on a page were she read for a few minutes before looking up, "I think my mum was an ancient."

"What!" was Rodney's shocked answer.

"That can't be possible, they are all gone aren't they?" asked Ronon cautiously.

"Well, they're not gone, they have mostly ascended to a higher plane of existence. But we have met some that haven't or who have retaken human form," said Sam.

"Rodney, do you have any pictures of the ancients that lived here?" asked Sophie whose mind was racing.

"Err yeah, I'll go get a laptop with them on," and with that Rodney left.

Sophie then turned to Teyla, "Teyla, in my quarters under my bed there is a box of photos, could you bring them please?"

"Of course, John, will you come with me?"

He nodded and followed her out of the infirmary.

"I've got to go check some stuff on the database, I'll be in my office if you need me," Dr Keller said.

"Colonel, if you don't mind me asking, I know you have had some experience with the ancients… when they…when they ascend is it a bright pure white light that rises from the body?" asked Sophie.

Sam looked thoughtful, remembering when they lost Daniel. Sam nodded, "I take it you saw it."

"Yes when I was young" Sophie explained of her mother's sudden deterioration of health and the night she died- her dream from the previous night. At the end of telling Carter and Ronon she could feel tears begin flowing down her cheeks. Ronon reached across and held her hand in a grip as firm as it was soft.

Sophie tried to regain her composure and by the time Rodney came back with the laptop, and Teyla and John came back with the pictures, her face was completely free of tears but Ronon's hand was still gripped around hers. He had however to relinquish his hold when McKay put the laptop on the table over her bed, so as to allow her to search through the pictures.

While Sophie searched through the pictures everyone was silent. Ten minutes into the search there was an audible gasp. Everyone looked over at Sophie who had fresh tears flowing down her face. She stared at the picture for a moment before turning to her box of photos and pulling one her mum and dad out. Then she turned the laptop around and showed everybody the person on screen and put the photo next to it. Everyone in the room moved closer, they where all trying to get a good look at the pictures.

It was clear even at a glance that the young dark brown haired girl in the photo was the same as the ancient from the laptop. The room was silent; Sophie was half ancient, but how? They were all gone and there certainly wasn't any alive when she was born especially on earth. There couldn't have been could there?

"I don't get it. How is it possible?" Ronon asked looking to the rest of the group for answers."

"Well, we have met ancients that have been sent back after ascending. We do know it is possible for them to retake human form, so its possible…"

"Ah, you're speaking of when Dr Jackson died, a year later you found him on another planet, with no memory of who he was." Rodney said interrupting Sam, who looked at him with a flash of annoyance, which Rodney chose to ignore.

"Yes Rodney thank-you for that. Anyway he had broken one of the ancient's highest laws and was banished back to human form." Said Sam taking over the conversation again.

A blinding white light suddenly filled the room. It gathered in the middle of the group at the foot of Sophie's bed. The light dimmed and when it was gone all that was left was a woman, with dark brown hair and who was beautiful. She smiled at Sophie and just sat there staring in shock.

"Mom?" She said quietly almost to her self. The woman was indeed the one out of the pictures.

She smiled at her daughter walking over to her and giving her a hug.

The woman looked around at all the people staring at her "I must apologize for the intrusion; I am Triyana, Sophie's mother. I am here because it seems I need to explain a few things." She looked to Colonel Carter as if asking permission and when she nodded Triyana continued.

"I once lived here as you know. I was among those who went to Earth. I, as you call it ascended, but like others found the no interference rule difficult to live with. I was banished down back to human form to pay for what I had done. There I met your father, Sophie. We married and had you. I then became ill with a disease you call cancer. It was incurable. They let me back when I died and they gave me another chance. As much as it pains me to just watch what the wraith and others have done, I have had the pleasure to watch my beautiful daughter grow up."

"I…I, err…I don't know what to say." Sophie said with tears filling up her eyes, unable to hold back her emotion.

Triyana smiled, gently wiping the tears that had fled from Sophie's eyes away.

"We'll wait outside." Said John, indicating that everyone should leave.

Tyiyana however looked at him and said "No, you all need to hear this."

John nodded and saw McKay and Carter exchange worried glances.

"Atlantis has dark times coming, each and every one of you are going to be essential in saving it, allowing it to live on. There's a force out there, like no other. You must prepare yourselves for what will be the greatest battle of all. It will affect not only this galaxy but every single one out there. You must not fail, it all rests on you." Explained Triyana.

"What's coming? How do we fight it?" Mckay asked quickly, panic creeping into his voice.

Triyana looked sad "I cannot explain more. I am as you would call it 'walking the line' already. You must trust me. I am sorry." Turning to Sophie, "I'm sorry my daughter, you are the future you must learn what it is to be an ancient in Atlantis, just like John, only better." She gave John a cheeky smile, before turning and looking at each of the group in turn, pausing on Ronon she gave him a small nod that went unnoticed by the others.

Triyana turned back to Sophie "I know it must be hard Sophie but you have lived so long without me that you truly do not need me. I must leave. Good luck to you all" the last part was spoken to the whole group.

Triyana was enfolded back into white light where she disappeared.

Moments later Dr Keller walked in, "what's up with you guy you look like you've seen a ghost?"

"Actually we have," replied John.

"Oh," was all Jennifer said before continuing "Well I've looked over the results again and it looks like this DNA we found is just an extension of the ATA gene so technically that means you should be the best at using ancient technology."

(A/N: Ok so this is all I have written so far. If any one has any ideas or things they want to see in it let me know!

As usual if there are any comments please leave a review (I like reviews!)

So tell me if you like it. I am at the moment considering taking this into a series with several parts to it. Is this a good idea?

Thanks For reading!!)


	11. Chapter 11

Stepping out of the wormhole Sophie felt relief flooding through her, this was it

1 month later

Stepping out of the wormhole Sophie felt relief flooding through her- this was it. She was home. The past few weeks had been so busy that Sophie hadn't had to the time to stop and think, especially about what her mom had said.

Looking round, she felt happiness swell as she saw her friends coming towards her. She had missed them all so much while she'd been away and was so glad to see them.

Handing the bags she came with to the waiting airman, Sophie turned to the approaching group with a grin filling her face,

"I'm back! Missed me?" she exclaimed

"Of course Sophie, it's good to have you back!" Teyla said warmly as she pulled Sophie into a hug.

When Teyla released her, John reached in and pulled her into another hug while saying "I'm really sorry you're gonna have to work with McKay, but its great to have you back, and if he causes you any problem…"

"I'll threaten him. Don't worry!" Sophie said laughing.

"Yes well it's good to have you back Sophie. I was thinking we could start our work in, oh lets say an hour?" said McKay, eager to get to work.

"McKay, she's only just got back, I believe it is better for her to get settled in before she begins work again," reasoned Teyla.

Sophie smiled at Teyla, before turning to Colonel Carter.

"Welcome back Sophie! Go get settled back and you can start your work with McKay tomorrow. Oh, and Dr Keller wants to see you when you have a minute," Sam said with a smile.

Now that the greetings were finished they all began excusing themselves to go back to their work. It wasn't till they had left that Sophie noticed Ronon for the first time. He had hung at the back of the group.

Feeling nervous Sophie walked up to him, indicating to the airman to take her stuff to her quarters.

"Hey," she said shyly.

"Hey," he said his low voice rumbling through her whole body.

She had missed him more than she dare admit.

"So, do you wanna do some sparring later that is as long as I get the all clear from Jennifer?"

"Sure," he said a small smile touching his lips.

"Well I shall see you later then." Sophie said and started leaving, before a gentle hand on her arm stopped her. She turned to see Ronon gazing at her intensely with his deep eyes, then with a swift movement he pulled her into a tight hug whispering in her ear,

"I'm glad you're still around."

Then as suddenly as he grabbed her, he let her go and left the room, leaving a surprised Sophie in his wake.

When Sophie arrived in her quarters she flopped onto her bed, deciding to unpack later. Her thoughts drifted back to the day in the infirmary. Her mind had gone over it a million times and tried to rationalise what she had seen. In the end she given and accepted it as a blessing.

However, she was still troubled though as her mom had referred to 'dark times' that were coming and a 'force like no other' - what was coming? Would they ever be ready for it? She knew it had worried everyone, that's why she'd been called back to earth.

While the IOA basically tried to decide what to do with her, Sophie began missing the home she had found on Atlantis. After much deliberating she had finally convinced the IOA that she would be more helpful back there. So they sent her back to help McKay discover new systems, as with her being half-Ancient she would no doubt be able to access much more of Atlantis. All they could do was prepare for what was to come and Sophie had every intention of winning the coming battle – whoever it was with.

Later that day Sophie arrived in the infirmary. Dr Keller greeted her enthusiastically and then proceeded to prod and poke her before giving her a clean bill of health and the permission to go spar with Ronon.

As Sophie left the infirmary she wondered where Ronon could be. Looking at her watch and seeing that it was already lunch time, she figured her best bet was the mess hall.

Upon arriving she saw Ronon sitting alone eating. After picking up her own tray and filling it with her lunch, she walked over to his table and sat opposite him.

"Mind if I join you?" Sophie asked politely.

After receiving a nod from him she settled comfortably into the chair and began eating her own lunch.

"So Dr Keller gave me a clean bill of health. Wanna spar later?" asked Sophie after a moment.

"You sure up for it?" asked Ronon with mock concern.

Sophie just rolled her eyes "I'm fine. You're just scared. I'm gonna beat the crap outta you."

Ronon looked up from his food and gave her a mischievous grin, his eyes glinting with the cheekiness of his expression. "I know I'll win!"

Sophie shook her head at him "You haven't got a chance...AH!" She yelled as he through a piece of food at her. Of course Sophie retaliated, which caused a full-fledged food fight.

Both Sophie and Ronon were covered in food when Sheppard, Teyla and McKay joined them.

"Hey! What the hell's going on here?" John demanded, yet with a hint of amusement in his voice.

"Oh…err…um…Sorry, Colonel…" Sophie stammered out, a sheepish look on her face. Until she saw John laughing at them, so she threw the food she had in her hand at him. This caused Teyla to erupt in fits of giggles, until Sheppard glared at her.

"Maybe, we should just go get cleaned up?" Ronon suggested to Sophie who was now laughing at Teyla as she watched the woman attempt to stifle her laughter.

An hour later Sophie walked in to the gym with Ronon, both clean after having changed their clothes and showered.

They began there fighting as normal, both whirling around simultaneously attacking and defending. After a while Sophie started looking at Ronon while fighting with him, really looking at him. There was so much she didn't know about him, so much she wanted to ask.

"Ummph!" Sophie tried to catch her breath as she landed flat on her backside after being knocked over by Ronon.

"You stopped concentrating Sophie," he said, that mischievous grin gracing his lips again.

"Yeah, next time I wont," she said as she got up off the floor standing in her fighting stances preparing for another round.

This time she had a plan.

As Ronon completed the same maneuver as last time, Sophie felt herself starting to fall and grabbed Ronon bring him down on top of her.

Giggling as they hit the floor she smiled saying, "and you shouldn't use such predictable moves."

A strange look crossed his face, and then he smiled placing his hands either side of her shoulders. Leaning down close to her, but mindful of not crushing her with his body weight, he whispered in her ear, "This predictable enough?" before kissing her lips delicately.

Neither heard the door of the door of the gym open until they heard "OOPS!" come from the open doorway. Colonel Sheppard stood opened mouthed.

"I'm sorry," he mumbled before walking away leaving the two of them in peace.

As the door of the gym closed, Sophie was already pushing Ronon off and standing up, her cheeks flushing with embarrassment.

"Sorry, I've…err…gotta go. I'm late for McKay." Sophie said as she practically ran out of the door.

"Sophie Wait!" Ronon yelled after. But just ignored him and continued back to her quarters.

(A/N: Thanks for reading! Please leave a review! And a massive Thank-you to Journeyman07! )


	12. Chapter 12

Hi Jayne

Chapter 11

When Sophie awoke the following morning her thoughts immediately drifted back to the previous day's events. After running from Ronon, she had hidden in her quarters for the rest of the night. She had curled up on her two-seat sofa and watched through her window, just staring out past the city and into the ocean.

Sophie had been watching the beautiful sunset when her door had chimed and firm but gentle shout of "Sophie?" had come from outside. She knew she couldn't hide from Ronon forever but, she was at least willing to try to, for now at least.

Ronon had spent a long time outside her door, knocking and demanding for her to open it. She needed time to think time, to understand.

As she rolled over and reached to turn off her alarm, Sophie was already dreading the day. Taking her time showering and dressing, she planned a quick breakfast by grabbing it and eating it on the way to McKay's lab.

Thirty minutes later Sophie walked into the mess hall, grabbed a bottle of water and some breakfast items before heading straight back out. As she was walking out she could see Ronon, who was sitting with John and Teyla, staring at her - an unreadable expression on his face.

Sophie hurried off to McKay's lab eager to set her mind on something else so she could avoid thinking about Ronon. Entering McKay's lab she could see both Rodney and Dr. Zelenka positioned round the same laptop, each talking over the other, both fighting to get their ideas out first. Both stopped though when they saw Sophie in the doorway.

"Sophie! How nice of you to join us. Maybe now we can get on with some actual work, instead of me constantly having to tell Radek his ideas are rubbish, "Rodney jibed in his usual smug manner.

Radek simply muttered what Sophie guessed were expletives in Czech.

Sensing another argument might erupt between the two men, Sophie said, "So where do you want me?"

"In the infirmary, Jennifer is going to hook you up to some machines to measure your brain activity while you are using Lantean based technology," Radek earned himself a glare from Rodney for this.

"Right, well I shall head on down there then," Sophie replied before walking out the room and not giving them a chance to say anything.

When she arrived in the infirmary, she glanced around the room, looking for Dr. Keller. Sophie saw her at the other end of the infirmary patching up a marine who had a cut to his face.

Keller saw her and said, "Sophie, just take a seat on that bed and I will be there in a moment, "and she pointed at an empty bed.

Sighing, Sophie sat down; this was going to be a long day.

It was well into the evening when Sophie finally left the infirmary. She made her way straight to the mess. Looking around as she entered she saw that it was empty apart from a few people dotted around at different tables. Smiling at the thought of some peace and quiet, she filled her tray and sat at the back.

Sophie had only been sat there a few minutes revelling in the quiet when a tray was put down and someone sat in front of her. Looking up Sophie felt her stomach begin churning as she tried to avoid Ronon's penetrating gaze.

"So…you wanna explain?" asked Ronon, looking straight at Sophie keeping his expression neutral.

"I just can't do this," Sophie managed to say before running from the mess hall. Too many times in her life had she lost the people she was closest to, and as much as she cared for Ronon, she didn't want him to get hurt. So Sophie thought pulling herself away from him would be the best thing for him.

She ran to an empty section of the city where she had been many times before. This balcony was where she felt at peace and the most relaxed.

When a hand gently touched her shoulder, Sophie whirled round ready to attack.

"I followed you. We need to talk," Sophie could see the urgency in Ronon's eyes and figured she had no choice.

Taking a deep breath she prepared herself for the discussion ahead, "I'm sorry. We can't be together…"

Ronon opened his mouth to speak, but Sophie raised her hand effectively cutting him off.

"I need to explain this so just let me," when Ronon nodded, Sophie leaned against the railings and looked out across the city, 'all my life anyone I have gotten close to has left me, and I like you…a lot and I don't want that to happen to you. I'm cursed I'm sure of it. Anyone I'm close to is always taken away from me and I tried to convince myself not to like you, but I can't its too hard."

Ronon moved next to her leaning against the railings and looking at her. Sophie looked into his eyes and for the first time she saw the guarded secrets behind them. She had known of his past as a runner, how he was one of the last of his people, but she never thought how difficult it must be for him. She wondered if he had left anyone behind.

"I spent seven years as a runner and I thought the same as you do. Then Sheppard and his team found me welcomed me here and they saved my life. I now have a family again, even though we are not blood related, we are a family. Me and Teyla like almost like blood relations. So, don't you see, I'm not going anywhere, I promise."

He pulled Sophie into a hug while she cried.

After a few minutes when Sophie's sobs had subsided, she leaned away from Ronon and looked up in his eyes and said, "I'm scared though. I don't wanna lose you and then there's this big threat coming that we know nothing about."

"I know but we'll be ready and we will win. But about us…we'll take things slow ok?"

Sophie smiled feeling much more relaxed, "Ok but can we still do this, I mean it's not to fast is it?" and reaching up she wrapped her arms round Ronon's neck and kissed him.

Ronon let out a low growl and said simply "No!" and began kissing Sophie again.

A/N: OK sorry this was a long wait. I hope you enjoyed this and I know it was only short. I have a lot of very important exams starting next week and lasting into June, so I may not be able to update for a while. But if I get a lot of reviews I may be convinced to update quicker!

Once again thanks to journeyman07!!

Hope you liked and don't forget to review!!

Thanks!!


	13. Chapter 13

As Sophie strolled into the infirmary the next morning, she felt much more relaxed than the previous morning

As Sophie strolled into the infirmary the next morning, she felt much more relaxed than the previous morning. Even though she was still a little nervous about her and Ronon's relationship, they had decided last night that for the time being to keep their relationship a secret until things were a little bit more settled and they knew where their relationship stood.

Glancing round the room, her eyes sought out both Dr McKay and Dr Keller, who where huddled around a screen in deep discussion. Unsure as to whether to interrupt them or not, she was relieved of the decision when Keller looked from the screen and saw Sophie.

Keller smiled and waved her over. When Sophie got closer she could see brain scans on the screen. There were two sets one that appeared normal and another that looked very odd. Sophie moved closer to get a better look. The other scan showed heightened activity in areas of the brain that where normally dormant. Sophie found her eyes searching out the patient name on the top of the screen, but not needing to, as she already knew. But there it was in the top left hand corner of the screen: 'Sophie Wells'

"These readings show that when you are using ancient technology there is something different. You could call it potential, but there is definitely something more to this other than just using ancient technology. I'm gonna run these readings against the database."

As soon as Dr Keller had finished speaking she walked straight into her office and shut the door.

McKay turned to Sophie and said, "I need to look at some stuff as well, so if you would just leave me alone I can get it done. I will radio when I need you."

Before Sophie got a chance to reply McKay had already left.

"What am I supposed to do now?" she muttered to herself.

"I could help with that," said low voice from behind.

"Ronon…" she said as she turned to face him, stopping when she saw a towel pressed on his cheek, with blood seeping through it.

"Oh!...what happened?" she asked moving towards him to get a closer look at his wound.

"I got my ass kicked by Teyla, she cheated," he said with a shrug.

Sophie laughed, "I can't imagine Teyla cheating, are you sure you didn't just lose concentration?"

Ronon raised his eyebrows and looked at her incredulously.

Shaking her head at him, she pulled him to a nearby empty bed and pointed at him to sit down. Ronon sat down, while Sophie went and collected what would need for treating his wound.

Sophie had nearly finished cleaning and stitching the cut on Ronon's cheek when he suddenly grabbed her wrist, making her jump.

"Have dinner with me tonight?"

Ronon was intently staring at Sophie as if searching her expression for a hint of her answer.

"Yeah OK, Id like that" she said with a grin.

'OK, calm down don't act like a freaking idiot in front of him,' she berated her mentally and forcing herself to finish dressing his wound without grinning like some crazy person.

It was late into a beautiful afternoon on Atlantis when Keller radioed for Sophie to return to the infirmary. Reluctantly she pushed herself from the railing of one the highest balconies in the city. She had stood there for the better part of an hour listening to the sounds of the ocean and looking out in to the distance, enjoying the complete tranquility of the moment. She knew that things were going to change soon and this dark force would come. She was also feeling the heavy burden of the entire expedition starting to rest on her shoulders; a thought that terrified her to her core. She knew Sheppard and his team would never rely on her alone, but she felt the responsibility all the same. If there was something she could do to help, anything, she wouldn't hesitate a moment.

"I'll be right there Dr Keller," she said and with one last look out to the ocean headed back inside, making her way to the infirmary.

When she arrived there Keller, McKay and Colonel Carter where waiting for her.

"Sophie after looking over your brain scans and looking at the Ancient database I believe we have discovered the reason for your err…abnormal readings…" Doctor Keller began before McKay tried to jump in wanting to say his piece, but was held silent by Sam's raised hand. Keller continued.

"…because you are for all intents and purposes half Lantean, you also share parts of their unique physiology. This means that you can use all the Lantean technology without hardly any concentration at all, it is like a natural ability."

By this point McKay was practically jumping up and down with his hand in the air like an impatient school boy - or someone who really needed to use the bathroom thought Sophie - that Colonel Carter lost her patience,

"Do you have something to say McKay?" she snapped.

"Yes actually I do. I think Dr Keller here is missing the big thing here. You see remember when some of the Lanteans came back, and basically kicked us out of Atlantis without so much of a thank you for getting it up and running for them again and basically keeping it safe from the Wraith even though we, well not me, but basically Sheppard or that, that Colonel Sumner woke them up, and did we even get a thanks for that no we just got a get out we want it back and…"

"MCKAY!" yelled Sophie, trying to break through his ramblings.

"WHAT?" he asked annoyed that he had been interrupted.

"Will you just get to the point already?" Sophie said much more calmly.

McKay looked towards Carter and Keller and seeing their frustrated glares, decided he would do just that.

"Sophie I think you can connect to the city."

'Connect to the city' what is he talking about she wondered? She looked and saw the other two women's faces, which showed a mixture of shock and disbelief, where she knew her own only showed confusion.

"What are you talking about McKay?"

Rodney sighed and gave her an'are you a complete idiot look' before just saying.

"You can create a mental link with the city and therefore control it, with your mind. You know using your thoughts."

"Whoa!" was all she could say before darkness enveloped her.

A/N: So I gave up on my revision to do this. So here you go it's just a little one to help develop the plot. I hope you enjoyed it and leave me a review if you like I always appreciate them!

As always a MASSIVE thank-you to Journeyman07 who is a BRILLIANT beta! Oh and she's forgiven for taking a while!

I'm gonna go and actually revise for my exams that I have tomorrow now!


	14. Chapter 14

Chapter 14

Chapter 14

When Sophie woke up, she found that she'd been put on one of the infirmary beds. At the foot of the bed stood Keller and McKay who were talking quietly. Sophie felt a blush creep into her cheeks as she remembered what happened. She had fainted like a child, how embarrassing!

"How are you feeling Sophie?" asked Dr Keller, her eyes showing concern

"Embarrassed, but other wise fine, I'm sorry I just fainted like that."

Colonel Carter took a step forward and smiled, "It's a lot for anyone to take in, don't worry about it. I think we should give you a few days to think about this and then I would like you to work with Rodney and try out this mental link. What do you think?"

"Yeah, sure." Sophie said in what she hoped was a confident voice because inside she was already panicking about the problems she could cause.

After Sophie left the infirmary she went to her quarters to get ready for her date with Ronon.

She now stood in a pretty green skirt and a white tank top, as she added the finishing touches to her make-up and giving her long straight dark brown a last brush. She had just finished when her door chime sounded.

As the door opened she smiled, Ronon looked even sexier than normal. His unruly hair had been put back and he was wearing jeans and a black shirt that showed off the top part of his chest. She knew he had got these clothes from earth and was surprised how good he looked in them, although he probably looks good in anything she added.

"Hi," she said feeling slightly nervous.

"Hey, you ready?" he asked smiling.

"Yeah, so where we going?" asked Sophie.

"It's a surprise; you'll see when we get there."

The walk was short and was filled with a comfortable silence. Sophie guessed they were nearly at the mystery destination when Ronon stopped.

Turning to her he said, "Close your eyes."

When Sophie hesitated he gave her a reassuring smile, "do you trust me?" Sophie nodded. "Close your eyes then."

After closing her eyes, Ronon gently led her by her shoulders giving her directions as she walked. Moments later a blast of warm air hit Sophie and Ronon stopped, taking his hands from her shoulders. He instructed her to open her eyes.

Sophie opened her eyes and smiled at the site in front of her. They were on one of the piers of Atlantis. And in front of her were a rug and a picnic basket. It was light so it was still warm. The rug was positioned so that when sunset came they would have a perfect view of it.

She turned to Ronon grinning, "It's beautiful, perfect."

"Let's eat then," he said grabbing her hand and pulling her over towards the rug.

They feasted on the array of food he had brought from the mess hall, talking all the time, discussing everything from Earth to Atlantis. They then sat together and watched the sunset. Sophie leaned into Ronon, who puts his arms protectively round her middle, and she felt completely at peace in Ronon's arms. The sun had just disappeared completely from the horizon when Sophie turned to Ronon,

"This is lovely."

Ronon smiled at this, planting a gentle kiss on her forehead. They sat for a while longer enjoying the peace before Ronon pushed Sophie up saying, "I have to be up early and so do you."

Feeling a little disappointed that it was going to have to end so soon, Sophie nodded her agreement. They collected all their rubbish and half eaten food, put it away in the basket and folded up the rug. Ronon then offered to walk Sophie back to her quarters, and hand in hand they set off.

When they reached Sophie's door Ronon gave her a quick peck on the lips before bidding her farewell for the night.

Laid in bed later that night, Sophie thought back to her wonderful evening with Ronon. She couldn't remember ever feeling so relaxed in someone's company for a long time. Her thoughts however soon turned to events earlier that day. She found herself still trying to wrap her mind around the thought of being able to link to the city. What if she did and she broke something like, the shield?

'Oh no!' she thought, or what if she overloaded the ZPM? Panic began setting in; she could not do this- perhaps she had better tell Colonel Carter of these concerns?

What if she accidentally linked with the city, and again caused problems? She would have no idea how to control the link and could end up causing even more problems trying.

The decision was made and she fell asleep deciding to tell Colonel Carter first thing in the morning.

Sophie felt slightly nervous as she sat in the briefing room waiting for John, Teyla and Ronon to arrive. Drs Keller and McKay and Colonel Carter sat around her at the table. Both McKay and Keller had laptops in front of them.

When Sophie had knocked on Colonel Carter's door earlier she had been nervous but the colonel had been very supportive and had called Sheppard's team to inform them all of what had been discovered yesterday and Sophie's decision.

The briefing room door opened and in walked John, Ronon and lastly Teyla, each of them taking seats at the table. Ronon gave Sophie a small smile, which she returned blushing slightly.

"So Colonel, what's going on?" Sheppard asked curiously.

"Well I'm going to let Drs Keller and McKay explain this to you," she replied with a pointed glance at the two doctors.

McKay immediately took the lead, "as you know we discovered Sophie here is half Lantean. So we decided to run some tests to see how well she could use ancient technology."

"And can she?" Sheppard inquired.

"Yes, yes, very well, now if I may continue without interruptions, all questions can be asked at the end." McKay continued, receiving an eye roll from Sheppard. "So we found she could easily use ancient technology without even having to concentrate. Dr Keller also ran tests while Sophie was doing this so as to help us discover more about the ancient gene."

"So I'm taking it you discovered something Dr Keller?" Teyla asked politely.

Dr Keller stood up moved towards a screen positioned at the other side of the room.

"If you look at this," she said switching the screen on, "this shows the amount of activity in a normal human brain such as mine or anybody here on Atlantis. But this…" she pressed a button on a remote she holding, causing the screen to change. It was the same as the last one, but had a lot red covered areas that had not been there before. "As you can see this shows a lot more activity, way more than it should be from any normal human being. This is the brain scan of Sophie when she is using ancient technology."

"What does this mean then?" Ronon asked.

"Well in all my time as a Dr I have never seen anything like this." Said Keller

"But I have." All eyes turned on Rodney. "After we found this, I searched the ancient database and discovered similar scans from actual Lanteans. Anyway with Jennifer's help I discovered that the areas in the brain that show more activity are to do with perception."

"Get to the point McKay, what does this mean for Sophie?" said Sheppard impatiently.

"She can create a mental link to the city, much like those Lanteans who came back and who where then killed by replicators could."

This time all eyes turned on Sophie.

Colonel Carter stood up and McKay and Keller both sat back down. "I gave Sophie a choice to not try this or to try and control the city. She came back to me this morning, she is going to do this and she is going to need everyone's support. Teyla, because we believe that this is similar to your Wraith abilities will you give Sophie some…err… training in mind control?"

"Of course, we can start when ever you want Sophie," Teyla said with a smile.

"Ok then, if that's everything I want to get all heads of department in here so they can brief their staff on this." Colonel Carter said, basically ushering them all out.

Later on Sophie was sat eating in the mess hall aware of the gazes that were being positioned in her direction. She was just about to leave when Ronon sat down.

"Are you ok?" he asked.

"Yeah I'm fine, other than everybody's staring at me like I'm some kind of science experiment. I'm sorry I didn't tell you about it sooner but last night I didn't want anything to get in the way of our date. I hope you understand."

"I understand, it was your decision to make but remember I am always here for you to talk to." He said, but Sophie could see through the calm deep voice and the guards behind his eyes, he was still concerned for her. Choosing to ignore it though she said,

"Thanks." he reached over giving her hand a quick squeeze.

"So, how does it feel to be the centre of attention?" Sheppard said as he put his tray down next to Ronon's.

"Don't be so mean John." Berated Teyla as she put her tray next to Sophie's.

"He's got a point though, everyone is looking at her and they're probably all talking about her too." Said Rodney as he shoveled food into his mouth.

"Rodney!" said Teyla with a glare as he sat the end of the table near John.

It was just as they where all finishing their meals and happily chatting, that over the cities communication system came the announcement.

"Could Colonel Sheppard and his team and Dr Wells all report to the control room immediately."

They all pushed their chairs back and ran out of the mess hall without saying a word, apart from McKay muttering under his breath, "what now?"

When they reached the control room, they could tell by Sam's face it was bad and when she moved out of the way of screen that she was standing in front of they saw the problem.

Everyone was thinking it but it was John, who voiced it,

"Crap!"

A/N: Ok so heres another chapter I hope you like! It's a bit of a cliffhanger, I know, but do you think you know what's they've just seen? Hmmm well again I appreciate any comments, thanks for reading!

Also THANKS to journeyman07 my brilliant Beta.


	15. Chapter 15

"Oh no, this is bad, really, really bad

"Oh no, this is bad, really, really bad," said McKay moving off to a nearby work station, where he furiously began to type, mumbling curses under his breath every so often.

"Am I missing something?" Sophie asked looking at all the worried faces that filled the room.

Sam turned to her and indicated to the screen that was showing three blobs. "This is Atlantis's long range scanner. We have just picked these up."

"So there are three ships heading to Atlantis?" when Sam nodded Sophie continued, "Is it the Wraith?"

"No, it's not the Wraith." McKay said without even looking up from the screen in front of him.

Now it was everyone's turn to look confused,

"If it's not the Wraith then who is it?" Ronon growled.

"Is it replicators?" Teyla asked.

"Oh I hate those guys." John complained.

"Will you guys shut up and listen to me! Its not Wraith or Replicators." Yelled Rodney

John, losing his patience, snapped, "Well who is it then?"

"I don't know, they are completely different to anything we've seen so far. Sam, we're gonna have to check the database, see if we can find anything out."

"Ok" She said before turning to face everyone else, " we don't know if these guys are friendly, so I want all of you working on this, Ronon work with them, see if you can recognise the ships. Teyla, I want you to help as well, but I want you and Sophie to work on the connection to the city. Rodney, I want you to split your work between identifying the ships and helping Sophie. John get together with Lorne. I want military strategies as well. If you any of you need any help from anyone in this city pull them off what they're doing, this is top priority. McKay what's the estimated arrival time of the ships?"

"We've got three weeks."

"Right, you all know what you need to be doing so I suggest you get on with it."

As everyone was leaving Teyla said to Sophie "We can go over some meditation techniques in my quarters now if you want?"

"Yeah ok I'll meet you there in a minute." Sophie replied.

When Teyla had walked off, she went over to where Ronon was quietly waiting to speak with her.

"Are you ok?" he asked with a hand on her arm.

"Yeah why wouldn't I be?" she asked.

"Well this connection to the city thing…?"

"Oh, no seriously I'm fine; we probably won't ever need it. I gotta go meet Teyla. Maybe see you later?"

"Yeah" he said before leaning down and giving her a quick peck on her lips, and began walking off in the direction Sheppard went.

Sighing quietly, Sophie put down her fork, knowing she was not going to be able to eat anything. She had spent her afternoon practicing meditation techniques that might be helpful in controlling her connection. Glancing round she could see the mess hall was really quiet, much quieter than normal at this time. There were a few people sat alone like her, and a few small groups. Most people where eating quickly with worried looks and some were sat staring out into space.

They had been here before, each person who had been on Atlantis a while knew what was coming, knew how bad it might get. But it still shocked them every time it happened. The feeling of panic, the fear. Maybe it got better each time they went through it, but looking at everyone's faces she could see the pain there, the loss of friends, colleagues and the thought of never seeing their families again.

I'm one of the lucky ones thought Sophie, the first time I've had to face this and I have nobody to lose. Ronon, he was her family now, was that too soon to say that? Was she rushing things?

Groaning she rubbed her eyes, jumping when McKay spoke in her ear "Dr Wells, report to the control room immediately!"

Sighing more loudly this time she pulled her self out of her chair, and dumping her tray on the way out, she left for the control room.

When she arrived, it seemed straight away that she was manhandled by McKay towards the gate.

"What? Hey! McKay will you let go of me!"

"Shut up this is important." McKay said before John came down the stairs behind them and said "Rodney will you calm down!"

Ignoring John Rodney ordered, "Stand here"

"Ok, ok. Jeez!"

Sophie moved to where Rodney was pointing in front of the gate, facing the stairs she could see Sam, Teyla and Ronon heading towards them.

"Ok, so when the Ancients we rescued came back to Atlantis one of them activated a console here and used it to take completely over the city. So I want you to try and access the console." McKay said in a much calmer tone.

"Sophie, remember what we did this afternoon, close your eyes, open your mind, let it seek out what you search." Teyla said in her soothing voice.

Nodding, Sophie closed her eyes, willing herself to open her mind, not even thirty seconds had passed, when she opened her eyes and frowned at the floor.

"Its not working," she complained.

"Keep trying and don't think about it so much, remember to clear your mind."

Sophie began again and this time lights lit up showing the edges of the console in the floor. But almost as quickly as it lit up, it was gone again. Sighing Sophie began again.

An hour later, Sophie was still trying, the lights had now lit up several times staying on longer each time, but nothing had happened for the last fifteen minutes and beads of sweat were forming on Sophie's face.

"Ok Sophie, let's call it day now." Colonel Carter commanded.

Sophie opened her eyes and nodded in disappointment; she looked at Rodney and saw his face drop.

"I will keep trying in the morning," she said before walking away and heading to her quarters.

Sophie headed straight into the shower, allowing the hot water to soothe her pounding head. She stood under the running water for a long time before getting out and dressing.

She had just settled in her chair near the window when her door chimed. Getting up, she answered the door, smiled a tired smile at her visitor, and then moved away from the door to let him in.

"Are you ok?" Ronon asked quietly.

"Yeah I'm just a little tired that's all."

"Yeah, look about that don't put too much pressure on yourself, it's not a good thing to do. We don't know that we will need you to control the city. So just promise me you won't beat yourself up about it."

"I wont don't worry, now I'm going to go to bed ok?"

"Yeah ok, I shall see you tomorrow then, sleep well," he said, then kissed her and left.

Sophie sighed and climbed into bed.

It was nearly three in the morning when Sophie finally gave up on sleep. She had tossed and turned for hours but still sleep had eluded her. So she had dressed quickly and left her room.

Atlantis was quiet at this time with only the people on night shifts around. As she walked towards the gate, she glanced to the control room. There were a few people there, but they all had their backs to her. She walked up to the spot she had stood before, closing her eyes and trying to clear her mind. Time became unknown to her and after what felt like minutes she heard low rumble. Opening her eyes she saw the ground just in front of her shake slightly. She immediately closed her eyes again and concentrated on thinking about the console coming out of the floor.

Sophie felt her mind begin to open- the rumbling grew louder. Sophie opened her eyes again, smiling as she did so - the console had risen out of the floor.

On the console there was space for a hand. Sophie reached down and pushed her hand into the space. Instantly images, numbers and all kinds of data filled her mind. She began trying to sort it out by looking for certain things but she found the amount of information too much. Her head started to hurt, she began feeling dizzy and noise filled her ears. She opened her eyes, looked at her hand on the console and pulled it away, pushing both her hands over her ears. Squeezing her eyes shut again she waited for the noise and information inside her head to subside.

When it did she moved her hands away and opened her eyes. Sophie gasped, she was sat on the floor, the console gone. But there were five concerned faces looking down on her.

"Sophie, are you ok?" asked Colonel Carter as she moved forwards towards her.

"Yeah I'm fine…Did you see it? The console! I got to come out of the floor, I touched it but my head became so full I couldn't control it, it was so noisy."

"You shouldn't have done it on your own, you don't know how dangerous it could be." Ronon said, with his arms crossed, clearly annoyed as well as concerned.

"Yeah, yeah. I know. I just couldn't sleep, sorry."

"Well now you have dragged us all out of bed, I'm going back there because I have so much work to do I don't know when I'm going to get any more sleep again," and with that Rodney left.

Teyla and Sheppard glanced at each other and then at Ronon who was still standing arms folded, glaring at Sophie who was glaring right back.

"Well we should all go back to bed, we can discuss this in tomorrows briefing. Goodnight, oh and Sophie please actually go get some sleep this time." Sam said before heading back to her own quarters.

John and Teyla also bid their goodnights before going their own separate ways.

Sophie began walking away to but Ronon grabbed her arm and pulled her towards him.

"Don't do things like that alone you could get hurt," he growled.

"I was fine Ronon. I knew what I was doing." Sophie snapped.

"Look you didn't know what could happen, what if when you took your hand off the console, the information didn't stop, it could have killed you Sophie."

"Didn't I just say I was fine." Repeated Sophie

"Fine" Said Ronon before walking off.

"Fine" Sophie shouted at his disappearing form.

A/N: Well I hope you liked that chapter, more about the ships in the next one!

But I have to just take a moment to say WOW!! I have had 50!! Reviews that is amazing, so I would like to thank everyone who has reviewed, added my story to their favourites, or has just read it! It means such a lot!

Thank you!

Well now I've said that I must go write the next chap, don't forget comments are appreciated!!


	16. Chapter 16

Ok this is not a full chapter

"Right, now everyone's here lets begin." Sam said looking round the room full of people, seeing no objections, she continued "Firstly, Rodney could you explain what you have discovered about the ships?"

"Thanks Sam," said Rodney as he moved to a screen at one end of the room.

Sophie sighed quietly to herself, preparing for the Doctor's presentation. She glanced round the room. Sheppard was sat in between Sam and Teyla, and next to Teyla sat a grumpy looking Ronon. A few people filled the rest of the seats. They included Doctor Zelenka, Doctor Keller and Major Lorne plus a few others that Sophie did not know.

Rodney began speaking so she turned her attention back to him once again.

"Ok so we ran what we could find from our sensor readings through the database and we found a match. They're a race of people called the Kali…"

"Wait isn't she a Hindu goddess?" Major Lorne asked.

Everyone faced him shocked, blushing he said, "What? I just know it, ok?"

"Anyway…" McKay said loudly in an attempt to bring the conversation back to him again.

"Hold on a minute Rodney, this Hindu goddess might give us a clue about what to expect, it's worked before. Major please tells what you know." Colonel Carter said.

Sitting up a little straighter under everyone's eyes his cheek still tinged with pink, Lorne began telling them what he knew.

"Well I don't know much. She is the goddess associated with death and destruction; however she was not a goddess of death but of time and change. That's all I really know."

John raised his eyebrows at his second in command who gave a small nervous smile.

"Anyway the database said they do not particularly interact with anyone, but themselves they live on a planet similar to earth. They are also described as technologically advanced, not as far advanced as Atlantis, but still it explains the reason why," McKay explained.

"The reason why what?" asked Ronon.

"The Wraith, they don't go any where near them, according to the database they haven't ever been culled," answered Rodney in a high pitched, excited voice.

"Wait, never been culled? Not ever?" Sheppard asked in disbelief.

"Never." Rodney grinned.

"I have heard of these people." Said Teyla slightly hesitantly.

"What do you know about them" queried Colonel Carter.

"They are as Major Lorne described, they leave death and destruction behind, but that is not their goal. Their goal is to ultimately keep things how they like it. I have never met them but they are well known of. The stories tell that they do not like things out of their control. Power is what they crave. It is very worrying that they are coming here. It is my belief that they do not like what we are doing in this galaxy, and they intend to stop us."

"How come I have not heard of them?" asked Ronon.

"I do not know, the stories are well known among my people, some however believed them to be a myth." replied Teyla.

"Ok Teyla I want you to work with Rodney's team to find out everything we know about them, if need be head off world." After receiving a nod of agreement Carter continued, "John work with them as well try and find out about weapons and the kind of fire power they have. Major Lorne I want you to organise the evacuation of non-military personal, I want them out of here three days before the ships are due to arrive. The Daedelas and the Apollo have been recalled as they are due in a few days. When they arrive we shall start a planning the defence of Atlantis. Right that's it I think. Everyone can go apart from Colonel Sheppard's team and Dr Wells."

As everyone else started heading out Sophie pushed herself deeper into her chair, awaiting the dressing down she was about to get.

When the room had cleared Colonel Carter turned to Sophie "Dr Wells, you seriously endangered your life last night. You must be at all times be accompanied by Dr McKay, or a member of his staff, when you try out these mental abilities. If not I will not hesitate in putting a security detail on your back."

"I understand." Sophie said quietly, her cheeks heating up, under everyone's stares.

"Right, now I believe you and Dr McKay have work to do."

"NO! NO! NO! Not like that! Do you ever listen to me? Don't answer that I already know the answer. How you people get put here I don't know. The best of the best, I don't think so. Just get out of my sight!" McKay yelled at the young scientist, who ran away like a startled rabbit.

Sophie turned to McKay, "Did you have to speak to her like that?"

"Yes it's the only way they listen" he snapped back.

Sighing Sophie turned back to the laptop. She had been sat at this laptop for the last few hours, familiarizing herself with the city's systems. It was boring work.

"You know McKay I think I have looked at this long enough can I try again now?"

"What? No! Just go take the laptop with you and make sure you understand all of Atlantis's systems by morning."

Sophie smiled, turned off the laptop and turned to McKay giving him a mock salute "yes sir!"

But he had already moved onto shouting at more of his team.

Dr McKay had done nothing but shout at people the whole time she had been there. It was rather off-putting actually. He had been supposedly looking at the systems for some kind of information about her ability to control the city. Although how he did any work at all was a mystery to her.

After dropping her laptop off in her quarters she headed to the mess hall for dinner.

When she arrived it was relatively empty, after grabbing some food she glanced around for somewhere to sit. She saw Ronon at the far end, sitting alone. They had not spoken since the night before. Taking a deep breath she walked over to him dropping her tray down in front of his. He looked up, she smiled and he went to get up.

Not looking forward to this conversation, Sophie gritted her teeth. Ronon had acted strange the night before, she didn't understand why he had reacted so aggressive, but she was here to apologize and maybe find something out. Here goes, she thought.

"Wait" she said laying a hand on his arm. He paused then sat down again. "I'm sorry. I was stupid, I know."

"You were," was all he said.

"I just wanted to be able to do this so that when these ships arrive I can help." She managed to stammer out.

Ronon raised his eyebrows at this "you're a civilian you will have been evacuated by then."

Sophie shook her head "I'm gonna volunteer to stay behind. I want to help. I will help."

Ronon's face grew dark, "So you're not sorry are you? You don't care if you put yourself in danger. You're careless with your own life. Well see if I care if you get yourself killed." He said angrily.

"Why are you reacting like this?" Sophie asked quietly.

"Because I will not sit here watch it happen again. I will not!" Relpied Ronon fiercely, before he got up and left.

Sophie stared after him, her eyes wide with shock.

"Are you ok, Sophie?" Teylas voice came through her clouded thoughts.

Turning herself to face Teyla. She answered sadly "No, I don't think so."

A/N: Ok so that was the latest chap and I hope you al liked it! Let me know! And thanks for reading!! A big thanks to journeyman07 who helped me out of the problem I had – an awesome beta!


	17. Chapter 17

Chapter 17

Chapter 17

Teyla smiled reassuringly at Sophie, who had just explained about her and Ronon's 'relationship' if that was even the right way to describe it. The 'relationship' had started and ended so quickly, but Sophie already missed it. Ronon was the first person she had begun to trust in a long time, he was someone, who she felt actually understood her.

'NO!' she thought to herself. She would not get like this, there was a city to save and if he was going to be unreasonable and glare at her with those, oh so gorgeous and deep eyes, not forgetting that rough, wild side of him.

She shook her head trying to turn her attention away from thoughts of Ronon.

"You should speak with him, Sophie. I am sure there is a very good reason for him to act the way he has." Teyla said purposefully.

"Hmmm, does pig headed count as a reason on your world?" Sophie asked.

"No. but I believe you should listen to his reasons, they are important."

Sophie turned and looked Teyla straight in the eyes, "I will not, he is the one that is overreacting." Sophie could feel the tears welling up, and threatening to break their banks.

"It is your choice. I was merely suggesting a course of action." Teyla said in her gentle, mothering voice. While putting an arm around Sophie for comfort.

The next two weeks went by in a blur for Sophie. She spent most of her time working with Rodney. Sheppard, Teyla and Ronon had gone off world several times to gather as much information on the ships as possible. Major Lorne had organised the evacuation, which had started already. The Daedalus and the Apollo had arrived also and were also helping to prepare for the on-coming battle.

The news from Colonels Sheppard's team had not been good. These Kali thought that Atlantis was causing too much change and that it should be sent back to the depths. This news was had not been welcomed by the Atlantis expedition, but it had certainly stirred people up: a new fighting talk began.

The days merged together. Sophie found herself sleeping very little; she didn't complain though, because she knew everybody was doing the same thing. When the evacuations began, however, Atlantis's mood changed and the excitement of the impending battle died down. It was replaced by fear. Most people wanted to stay behind, but it was decided that the ones who would be of most use, would stay. In Sophie's eyes this was unfair yet understandable. She had been allowed to stay - to fight.

Her control over the city was still nowhere near being useful. From the control interface she could control minor systems but no more. With a week to go Sophie was feeling the pressure. The only person she could talk to was Teyla and even though she trusted her, the one person Sophie really wished she could talk to was Ronon. He had avoided her like the plague since the incident in the mess hall.

Sophie walked to the gate room and watched as the last group prepared to leave and no one looking that happy to be going. She leaned against the railings watching the stargate being dialed. She had a bad feeling, a very bad feeling. This last day it had got worse as if something was nagging at her.

Sophie felt a shiver run down her back, then a hand touched her shoulder making Sophie jump she turned and came face to face with her mother.

"M…Mum?"

Triyana looked at Sophie, giving her a small encouraging smile.

"All is not as it seems." Was all Triyana said before disappearing again.

Sophie stood staring in to the space her mother had just vacated. The sound of the stargate shutting down jolted her back into action.

What had she meant? 'All is not as it seems?' it seems as though we have one week to prepare… "Oh no." said Sophie out loud.

Sophie ran down the steps straight over to the place where the control panel was. Without hardly any thought she activated it. Placing her hand on it and allowing the knowledge to fill her, immediately she began looking through the sensor data even if she was still struggling to pick it all apart.

It was there - what she needed but she wasn't glad. Sophie would have given anything to be wrong. But the mistakes had been made and Sophie hadn't spent the last weeks understanding Atlantis's systems for nothing. It was wrong and she knew it.

She pulled her hand off the control panel, and took a moment to catch her breath. She could see Colonel Carter heading her way, a displeased look on her face. Yet Sophie didn't care this was too important.

"Colonel, Colonel! We got it wrong very, very wrong. It was staring us in our face and we didn't see it!" shouted Sophie, feeling the panic begin to emerge.

Colonel Carter, now concerned, asked, "What have we missed? What's going on?"

"I'll show we haven't got much time…oh and get Dr McKay, NOW!" Sophie yelled over her shoulder as she raced to the control room.

As she got up there she could see Sheppard, Ronon and Teyla just arriving. McKay coming along behind them - already she could here him wittering incoherently.

Sophie walked straight over to the sensors. Calling everyone over she shouted "LOOK!" pointing at the long range scanners and pushing a guy who was working at that station out of her way.

"Looks like she's spent too much time with you Rodney" quipped Sheppard.

Which earned him looks from both Ronon and Rodney.

"Yeah! Ships heading our way. Due to arrive in a week! We know this shouldn't we be working on a way to defend ourselves instead of…." Said an irritated McKay.

"SHUT UP MCKAY!" Sophie said interrupting Rodney. "For once listen to someone else! You've made a mistake. Not just you, we all have and its been staring us in the face. These sensor readings aren't real. They're fake."

"Fake? Is it even possible?" Teyla questioned.

"Yes," said Sophie at the same time as Rodney said "No."

"Holy Hannah!" Carter said as she moved closer taking a better look, "Its so obvious. I can't believe we didn't spot it."

"What is?" asked John who was growing more concerned by the second.

"There's a wave of some sort going through it, if you watch the picture closely it appears to 'pulse'." Carter replied.

"Let me take a look," insisted McKay. As he leaned forward and looked properly he too could see it, "Oh my god! They've tricked us."

"How can we see the real screen then and how has this one appeared?" asked Sheppard.

"They must be emitting a frequency that jams the Lantean system but allows what they want to be projected on to the screen. We need to find out what it is and block it." Said McKay, as he started working on the problem

"I know it." Sophie said.

"What! How?" McKay asked practically speechless.

"I looked in the cities systems for any unusual signals and I found it all you need to do is stop it, by resetting the system. When you reset it the signal needs to be resent to take affect again. So we may have enough time to study the real readings." Answered Sophie, a little unsure of what people's reactions would be.

"I did not realise you had that much control yet." Teyla pointed out.

"Neither did I, but I saw my mum and she said all is not as it seems. I started thinking about what she meant and I thought what if it was something to do with the ships. So I checked the systems via the control panel."

"Wait, your mom was here?" asked Sheppard.

"Yeah but just for a second she just said 'all is not at is it seems' then left." Sophie answered.

"Oh no! SHEPPARD!" McKay yelled from his place in front of the sensor control panel, where he had just reset the system.

"What is it?" Sheppard asked stepping closer.

"We have a big problem! McKay said "They're nearly here!"

Instantly Carter's hand flew to her radio, where she contacted the Daedalus and Apollo, telling to them to get out of sensor range.

While Sheppard got all defence teams into position. But there was a problem Atlantis wasn't ready, it was too early.

"We're screwed!" said Sophie, realising her worst fears were here and were about to knock on the front door.

A/N: Ok I know cliffhanger not good. But I will update as soon as possible! Thanks for reading as usual and don't forget to eave a review! Thanks!

A


	18. Chapter 18

"Colonel, how are we going to play this

"Colonel, how are we going to play this?" John asked, tension seeping into his voice. "Shield or cloak?"

"I think our best chance is going to be cloaked and hope they don't find us. We will be vulnerable for a short time while switching over, but I think it's the best course of action. We don't to have to get in to a battle unless we really have to." Colonel Carter said, her voice conveying that she was also worried. "I've got to contact Earth. McKay, how long have we got?"

"Just under half an hour." He replied grimly.

"Right. John, take Ronon and get everyone in to positions. Teyla, Sophie, gather everything we know about these people and bring it here. We may get a chance to talk to them. McKay, make sure everything else is working properly." Carter ordered.

As soon she had finished talking everyone moved off quickly to complete their tasks, a sense of urgency filling the air.

25 minutes to go

Sophie and Teyla moved quickly back to McKay's lab where they had been gathering all their information. Moving swiftly they picked up all the papers and grabbed a laptop that contained most of the information. As they headed back to the control room, activity within Atlantis had increased; the remaining members of the expedition were gearing up and heading to their defensive positions.

18 Minutes to go.

Sophie and Teyla arrived back in the control room where McKay was once again shouting at the techs. Sophie shook her head at him before moving into Colonel Carter's office and setting up the laptop. Then her and Teyla began briefing the Colonel on all they had managed to find out.

8 minutes to go

Desperation began to set in. It had taken so little time to brief the Colonel about what they knew and most of that was speculation and stories. They didn't know what was coming. That was the worst part, the not knowing. Sophie looked out of Sam's office, the control room was bustling. But it was the looks on people's faces that really scared Sophie. It was that look of despair, it was all too soon and everybody knew it, they didn't stand a chance.

It was the low growl of "Dr Wells" that stirred Sophie out of her worries. She turned to see Ronon in the doorway. It was the first time he'd spoken to her since their argument and he hadn't even used her first name. That hurt Sophie more than she would ever be willing to admit. Pushing the thought to the back of her mind she looked at him and gave a polite "yes?"

"Sheppard wants you with us in the chair room." Sophie nodded and looked to Carter for approval, which she received from a nod, then followed Ronon out.

4 minutes to go.

They were just outside the chair room when Ronon stopped suddenly and turned to her, Sophie not expecting it nearly fell over as she crashed into him, if it wasn't for his arms holding her up, she probably would have done.

"We need to talk." Ronon said.

Sophie looked into his eyes and nodded. He then walked into the chair room, his expression a careful blank.

Sophie followed him, with mixed emotions. He wanted to talk, that had to be good right? But he had called her 'Dr Wells", now that was definitely not a good sign.

When she entered the small room, Sophie glanced around and the only thing that was in it was the chair, hence the name. Colonel Sheppard was sitting in the chair, his face was apprehensive.

He gave Sophie a nod of acknowledgement before saying,

"I wanted you here in case things went wrong, you might be able to access systems I cant."

Sophie just gave him a tight smile. Wishing so much that this wasn't happening, that things with Ronon were ok, that Sheppard wasn't here and Ronon could talk to her. She let out a small sigh a convey her annoyance.

As the minutes wore on Sophie felt the tension doubling. Radio communications where constant from the control to all listening, including the two now hidden ships. The city had been cloaked before the ships came into sensor range. It was now a waiting game.

Far above the city of Atlantis, three ships emerged from hyperspace. The announcement was made over the radios and all life froze. No-one dared move, this was it. It felt like judgment day, and the verdict was about to be announced.

A low deep, rumbling voice filled the halls of Atlantis for everyone to hear.

"We are Kali. We do not tolerate change that is not our own. You have undermined us. The decision has been made. We control change here, you ignored this and for this you will all pay the price. Your death will return our control. Do not fight it, you will lose."

Sophie glanced around her, as if looking for where the voice came from. Over the radio she could hear Colonel Carter trying to reason with the Kali, but all that was received was a harsh laugh that echoed through Atlantis.

The laugh contained no humour - it was hollow and evil. Sophie jumped at it, letting out a small yelp. This earned her a look from Ronon.

Seconds later the order was given for the shield to go up. It was too late though - the ships had already emitted some kind of pulse weapon.

Panic could be heard on the radio; Sophie could hear McKay yelling that the shield wasn't going to be up in time. The order was given to brace for any impact. Sophie moved back pinning herself to the wall. Taking deep breaths trying to keep herself calm. She prepared herself for the impact.

The impact never came; they were however plunged into darkness.

"Crap!" was Sheppard's annoyed response.

"What the hell was that?" asked Ronon

"There's no power going in to the chair! Colonel Carter, this is Sheppard, you there?"

No response

"Radios must be down too," he said pointlessly.

Seconds later the power came back but it was only very low-level lighting.

"Someone must have got emergency power working…"

John didn't get to finish speaking as something impacted the city, knocking them all to the floor. A loud explosion filled her ears and Sophie hoped that everyone was ok.

As Sophie looked up from her place on the floor, she could see Ronon already getting up. The room was still one piece at least. She glanced over to the chair, where Sheppard was. John however was lying now next to the chair unmoving.

"John!" Yelled Sophie, moving over to him. When she got to him she could see blood from a wound on his forehead. She checked him over, deciding that other than a concussion and a nasty gash he was fine. But she needed to bandage his wound. Pulling her jacket off she tried to rip a strip off it. It wasn't working, the material was too strong; a sound of ripping came from Ronon's position behind her. A piece of cloth was handed over to her. She thanked him and tied it round the colonel's head.

She had just finished when her radio crackled back to life. "Sheppard, this Carter come in please."

"This is Dr Wells, Sheppard's unconscious; he took a blow to the head."

"Ok then. It falls down to you Sophie, we can't access anything here the city has locked us out. We need you to use the chair to find us a way back in or at least get the shield back up. We need you to do this as no one else can; the city has locked itself down. Our ships have moved into position and are fighting but we can't loose Atlantis."

"I understand" Sophie replied.

She didn't move though she just stood staring at the chair.

"Sophie?" Ronon said moving towards her.

She looked at him "I can't do this, I don't know how." Tears filled her eyes as she felt the panic take over her.

Ronon stood in front of her and grabbed her shoulders, shaking them gently he said, "You can Sophie, you was born to do this. You said it yourself you've never felt happier here. It's your home. So go and save it!" He lent down towards her giving her the gentlest kiss on the lips before pushing her to the chair.

A/N: Ok another chap hoped you liked, Thanks for reading and please leave a review they are greatly appreciated and encourage me so much.

Big thanks to journeyman07 who for story has been an awesome beta, even though she can't continue to be so. She made this story actually readable!

The next chap will be up soon!!


	19. Chapter 19

Sitting in the chair Sophie cast a glace at Ronon, who was kneeling next to Sheepard

Sitting in the chair, Sophie cast a glace at Ronon, who was kneeling next to Sheppard. Taking a deep, calming breath she leaned back into the chair, closing her eyes.

Nothing happened.

The chair didn't activate, the systems didn't show themselves to Sophie. There was nothing.

Sophie snapped her eyes open and looked at Ronon, "It won't work." She said quietly.

"Sophie you have to do this, you have to make it work." He said forcefully to her.

She nodded her head and sat back again. Closing her eyes she put all her effort into powering up the chair. All she came across though was what she could only describe as a wall. Something was blocking her. All she needed to do was find a way round it.

Simple. Well…sort of.

Ten minutes later she was still trying to fight through the block in the system. Then a thought occurred to her, there must be a reason why this was happening.

Sophie almost smacked herself in the head as the realisation hit her. The Kali, they must somehow be affecting the systems; keeping us locked out and allowing them to attack. If it was the same as how they were affecting the long range sensors, all they needed to do was reset the systems.

Standing up from the chair, Sophie nearly fell over as another explosion rocked the city.

"Dr McKay, this is Dr Wells, come in please."

"Aren't you supposed to be…" came his lecturing voice.

"McKay, shut up and listen." Sophie then carried on relaying her thoughts and idea to him.

"Good idea but its impossible. Like not even a chance of working…unless…yes that's it! Sophie you are gonna have to disconnect the chair manually then reconnect it and reset the rest of the city from there, when your up and running."

"Ok, but you're gonna have to talk me through this." She said.

The next few minutes were spent frantically with Sophie following Rodney's instructions. But in virtually no time at all the chair was disconnected and was about to be reconnected.

"Let's hope this works," said Sophie as she plugged the last crystal back in and stood back to see a glimmer of power flow through the chair. Climbing back on with a new sense of purpose and confidence, she closed her eyes and this time her mind was filled with a surge of information. She could see that one of the Kali ships had been destroyed, but the other two were still battling Earth's ships.

She only glanced at this though before moving on to the task of bringing the city back under their control. Immediately she started resetting all of Atlantis's systems, including getting the shield back up and running. She deactivated the chair.

"Colonel Carter? You should have all the systems up and running now," Sophie said not moving from her place in the deactivated chair, her head spinning from the effort.

"Well done Sophie." Came Colonel Carter's voice. "There's just one more thing, I need you to use the drones." That was all that needed to be said. Sophie knew what was being asked of her. But could she do it? Could she live with the guilt of murdering all those Kali, aboard those ships? Even though they were intent on killing everyone in this city.

"Sophie?" came Teyla's low voice. "You have to do it. Think how many people will die if you don't. These Kali are sick and twisted and they're intent on murdering the innocent. You can't let that happen."

"Ok. I'll do it. Its just…I have never fired a drone before." Sophie said.

"You can do this Sophie." Said Teyla's calming voice again. Sophie found herself wondering how Teyla came to have such a calming influence over people.

With a quick glance at Ronon, who was still in his same position as before, watching over John, she received a small supporting smile.

Settling back into the chair and once again closing her eyes she focused upon one of the Kali ships, she then concentrated on firing a drone at that ship. There was a tense few seconds as she tracked the drone to its final destination, allowing herself a small smile when the first Kali ship blew up. Straight away she locked onto the next one without hesitating to fire. As soon as she saw that the last ship blew up she was out of the chair.

"Well done Sophie! We have a medical team heading to your position now. Just sit tight. Carter out"

Twenty minutes later the medical team turned up headed up by Dr Keller.

"Sorry it took a while, there's some damage to the city out there, and we had to go slow." Said Dr Keller as she took over with Colonel Sheppard.

Within a few minutes Keller had Sheppard loaded on to a stretcher and wheeled out of the room.

Sophie and Ronon walked together behind the medical team, taking in the damage as they walked.

There was quite a lot but none of it looked particularly structural, or so Sophie thought. That was until she took a wrong step on a loose piece of metal flooring on one of the balconies of a storage room which they had cut through.

The metal gave a tremendous creak then crack. Suddenly Sophie found herself falling. She screamed and tried to grab something to hold onto. She only found a sharp piece of metal, which sliced her hand as she grabbed it. Letting go because of the pain in her hand,

she felt herself fall the rest of the way. Feeling pain as she hit the floor, then nothing, as black over took her.

A:N A big thanks to Louise and Alex for this chap. Hope you liked! And the next chap is written I just need a beta before I can upload it. Leave a review!


	20. Chapter 20

Chapter 20

Chapter 20

The mood was somber; Atlantis' personnel filed silently into the gate room—military in their dress blues, civilians in their suits. These outfits were worn for both celebrations and those events that no-one wanted, like today. It had been three weeks since the attack from the Kali, and the entire expedition was now back on Atlantis. Their first order of business, though, was not a happy one. There was not a smile in the room, only tears and loss.

In the centre lay one pure white coffin, decorated with the American flag and a wreath of flowers.

The entire expedition had now entered the room and the service began. Colonel Samantha Carter spoke, telling all what a great sacrifice had been given by the deceased, "We owe them our thanks," she explained, emotion filling her voice. "Already we have lost too many people. Losing another is just as hard, if not harder. But this was not just a person. This was our friend, and they were part of our family here on Atlantis. It gives us all a great sadness to know that they are no longer with us. When we walk down the corridor we know there is now no chance of bumping into them for a quick chat. Not even chance for a nod of heads as we pass, nor a chance for an exchange of smiles. She showed us a bright side here; they made us smile and laugh. I know that each and every one of us has been in some way touched by them. We have one less person in our family now and I know that you all feel the loss greatly. I just hope we can all be there to help each other through this difficult time."

Sam gave a small nod to the control room, the gate began dialing Earth. The sound of the wormhole being created filled the silence. She then nodded to a group of people stood at the front, and led by Major Lorne they moved forward, and taking a hold of the coffin together they walked through the gate. While this was going on the sound of trumpets filled the room, echoing off the walls, straight into the mourner's hearts.

_Sophie glanced around; there was nothing to see other than pure white light. In front of her the white light began to congeal together, within seconds the form of Triyana had fully formed in front of Sophie._

"_Mum! Where am I? What's going on...Am...Am I dead?"_

_Triyana offered Sophie a sad smile, "Not yet."_

_Sophie looked down at her feet, taking a deep breath before looking towards her mother again, saying quietly, "You mean, I'm going to. I'm dying aren't I?"_

"_Yes" Triyana said solemnly._

_Sophie felt her eyes fill with tears. She didn't want to die she hadn't even gotten to say good bye…to Ronon._

"_But there is a way." Triyana continued._

_Sophie filled with hope. She could live again. "Anything! I will do anything it takes."_

"_You must give up that that makes you different. You will no longer possess the ability to connect to the city like you once could. You will of course still possess the gene, much like Colonel Sheppard, and it will still give you great power, but no more than others with the gene. I'm sorry. It is either this or death."_

_Sophie thought for a moment. There really was no decision to make. She just hoped that the rest of Atlantis agreed._

"_I wanna live." She said, her decision made._

_Triyana smiled. "I wish there was more I could do for you. This is good-bye Sophie. I will never be allowed to contact you again because of this. Be safe and be happy! Even though I know you will._

_Triyana then reached to give her daughter one last hug, but Sophie found herself hugging air. She allowed a single tear to flow down her cheek before she disappeared from that place._

"BEEP…BEEP…BEEP!" This rhythmic sound was the first thing Sophie became aware of, that and a throbbing in her head. She could feel a hand gently gripping on her own right hand.

Pain was also shooting up and down her entire body, meaning she couldn't work out where it hurt the most.

Groaning, she allowed her eyes to flutter open, only to close them against the harsh light of the infirmary. "Oww" she muttered.

"Sophie?" Ronon's deep growl sounded from next to her. "Doc! She's awake!" He yelled.

"Too bright" Sophie mumbled, struggling to speak due to the dryness of her throat.

She could hear footsteps approaching the bed. She tried to open her eyes again and found that the light had been turned down. Blinking the blurriness away, she looked to Ronon who had a grin on his face and was still holding onto her hand, only tighter now.

Doctor Keller walked over and shot Sophie a beaming smile while she moved around the machines to check that all of Sophie's stats were ok.

"How are you feeling?" Keller asked, with her perfected bedside manner.

"Thirsty…and pain…lots of it." Sophie managed to quietly grate out.

"Here," this did not come from the doctor. It was instead Ronon, who was holding a glass of water with a straw ready for her to drink some.

She gulped down the water greedily, causing herself to cough.

"Whoa! You might want to go easy there ok?" said Doctor Keller, as she collected a syringe from a nurse. She inserted the needle in to Sophie's IV.

"Morphine; for the pain," explained Keller.

Sophie nodded before asking, "What happened?"

"You were walking back to the control room behind the medical team, you accidentally stepped on some broken flooring and fell twenty feet. That was three weeks ago. You hit your head, and it caused some pressure on the brain. We had to put you in a medically induced coma until the pressure went down. Last week we took you out of the coma and have been waiting for you to wake up. You have significant bruising to your spine, so that's the main cause of the pain as well as a broken leg. Oh, and your hand sustained a nasty gash but that's healing nicely. Now I want you to rest as much as possible." Then with a pointed look at Ronon she walked away.

"How's Colonel Sheppard?" she asked.

Ronon's face darkened, instantly Sophie grew more concerned. "He's fine. Sergeant Wallis however didn't make it. He was hit with debris from one of the explosions caused by the Kali weapons. He died instantly."

Sadness filled Sophie. Sergeant Wallis had been on Major Lorne's team. He had been a really good guy, always making jokes. He didn't deserve to die.

"Major Lorne went back to earth with his body he wanted to tell his family himself." Ronon explained.

Sophie nodded, her eyes closing as she drifted off to sleep again.

The next time Sophie awoke a few hours later she felt much clearer headed, the pain wasn't as bad either. Ronon was still there as well, in the same position as he had been when she fell asleep, apart from now he was sleeping silently in the chair.

As if sensing that she was awake Ronon woke up suddenly. He smiled when he saw her and reached down to squeeze her hand. "How are you feeling?" he asked

"Much better." She said with a smile.

She wondered if he was still mad, then guessed he probably would be. Then there was the 'talk' he wanted to have with her. She wondered if he was going to do it here in the infirmary, she hoped not, that could be a little embarrassing. She shook her head of those thoughts; Ronon wasn't like that, he was too private.

"About that talk; we're gonna have it when you're better ok?"

_Whoa!_ She thought, had he read her mind. She gave a small smile nodding her head in agreement.

This was one talk she was not looking forward to having.

A/N: I hope this wasn't too confusing but I wanted to keep you all guessing! A big thanks goes to renisanz for being a fantastic beta! Don't forget to leave your commentsand thanks for reading!


	21. Chapter 21

Chapter 21

Chapter 21

After a few weeks, Sophie was released from the infirmary. Her hand was almost completely healed but she still had a little bit longer with her leg in a cast, but thankfully she was able to use crutches.

Sophie had spent a lot of time with Ronon while she was in the infirmary; he was like her constant companion. But the 'talk' had never been mentioned since that day, and Sophie knew that now that she was out of the infirmary there would be no escaping it.

So slowly, Sophie hobbled on her crutches to Ronon's quarters where she waited for him to answer. As soon as he opened the door he was at her side helping her and asking her why she hadn't gotten him to help her.

Once she was settled in a seated position on the bed with Ronon at her side, she took a deep breath. After about a minute, "So…you wanted to talk?" she asked nervously.

Immediately Ronon's face darkened, but he nodded his agreement.

"Why…why did you get so mad?" Sophie asked tentatively.

Ronon did not answer but instead looked uncomfortable.

"Come on Ronon, just tell me. I promise I will understand." She prodded.

All she got was more silence, with Ronon even avoided her eye, so she tried again. "Look, whatever it is, whatever you're worried about, you can tell me. I care for you and now I'm worried for you," she said.

This was not at all what Sophie had expected. _Why had he just frozen? Was it really that bad?_

Realisation struck Sophie like a bolt of lightning…_Sateda._

"Is it about Sateda? Did something happen there?"

Ronon looked up into Sophie's eyes and she saw pain, loss and…love.

"When Sateda was attacked…" he began, speaking in a barely audible whisper, "…I had a fiancée. Her name was Melena. She was a nurse. I had gotten her and me transport off Sateda, but… she wouldn't go. She said she was needed." He paused his face clouded with hurt and loss, it was weird seeing him so overcome, and Sophie realized that this must have been something very difficult for him to do; to actually talk about it.

Sophie took his hand giving it a gentle squeeze, giving him the strength to continue,

"She was killed right in front of me in an explosion."

"Oh my god, Ronon, that's awful. I'm so sorry."

"Do you understand now?" he said his voice stronger this time. "Do you understand why I did it? Why I got so mad? I couldn't bear to loose you like I lost her; I wanted to protect you and thought that I could do that by sending you away. But you wouldn't go, I couldn't make you leave. I didn't want to loose you." His gruff voice conveyed so much emotion and his eyes sparkled as he spoke, Sophie became a little overwhelmed at it.

Tears prickled Sophie's eyes. "Ronon, thank you, and I am sorry, but you have to understand it was my decision to make, as it was Melina's. It's not your fault you know."

Sophie smiled up at him and pulled him into a hug. She felt privileged to learn this from Ronon.

"You've not told many people this have you?" she asked curiously.

He shook his head.

She smiled up at him "this means a lot that you told me then, truly it does. I wanna be there for you like you've been there for me."

He was a private man—but a good man.

The threat from the Kali hovered over Atlantis for a few weeks longer than Sophie's stay in the infirmary. It was through tricky negotiations between Colonel Carter and Colonel Sheppard's team that the Kali agreed to leave Atlantis alone for now, under the condition that they didn't stray in to the Kali controlled section of the Pegasus galaxy.

Sophie and Ronon's relationship also grew and became the hot topic of gossip for quite a few weeks afterward. Although McKay was disappointed that Sophie lost her 'powers,' the readings he had gathered when she had them proved interesting. Sophie however was more than relieved to have escaped his clutches, although the constant 'are you sure you haven't still got some of it left?' was really beginning to bug her.

As she sat on her balcony, Sophie smiled as she reflected over those last few weeks.

She finally was at peace with herself, she thought back to before she came to Atlantis she hadn't been the same person then. Atlantis had changed her. She wondered if it did that to everybody. Maybe McKay wasn't such a know-it-all before he came to Atlantis? No she would have happily placed money on it that he was. Sophie looked out to the ocean; she had everything here friendship, happiness and a life.

Even a little thing called love.

The smile turned into a grin as Ronon reached his arms around her, turning her around and pulling her towards him. She sighed contentedly as he lowered his lips to hers.

.

The End.

A/N: So that's it its finished. This was my first fic and I just want to say Thank you to everyone who Beta'd (especially Renisanz for this chap) and everyone who read, reviewed, added to their fave list and alert list. I think I have developed as a writer during this and I hope you have all enjoyed it!


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